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Calayugan MIC, Hore TK, Palanog AD, Amparado A, Inabangan-Asilo MA, Joshi G, Chintavaram B, Swamy BPM. Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map. Sci Rep 2024; 14:18024. [PMID: 39098874 PMCID: PMC11298551 DOI: 10.1038/s41598-024-67543-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 07/12/2024] [Indexed: 08/06/2024] Open
Abstract
Developing high-yielding rice varieties that possess favorable agronomic characteristics and enhanced grain Zn content is crucial in ensuring food security and addressing nutritional needs. This research employed ICIM, IM, and multi-parent population QTL mapping methods to identify important genetic regions associated with traits such as DF, PH, NT, NP, PL, YLD, TGW, GL, GW, Zn, and Fe. Two populations of recombinant inbred lines consisting of 373 lines were phenotyped for agronomic, yield and grain micronutrient traits for three seasons at IRRI, and genotyped by sequencing. Most of the traits demonstrated moderate to high broad-sense heritability. There was a positive relationship between Zn and Fe contents. The principal components and correlation results revealed a significant negative association between YLD and Zn/Fe. ICIM identified 81 QTLs, while IM detected 36 QTLs across populations. The multi-parent population analysis detected 27 QTLs with six of them consistently detected across seasons. We shortlisted eight candidate genes associated with yield QTLs, 19 genes with QTLs for agronomic traits, and 26 genes with Zn and Fe QTLs. Notable candidate genes included CL4 and d35 for YLD, dh1 for DF, OsIRX10, HDT702, sd1 for PH, OsD27 for NP, whereas WFP and OsIPI1 were associated with PL, OsRSR1 and OsMTP1 were associated to TGW. The OsNAS1, OsRZFP34, OsHMP5, OsMTP7, OsC3H33, and OsHMA1 were associated with Fe and Zn QTLs. We identified promising RILs with acceptable yield potential and high grain Zn content from each population. The major effect QTLs, genes and high Zn RILs identified in our study are useful for efficient Zn biofortification of rice.
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Affiliation(s)
- Mark Ian C Calayugan
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, College, Laguna, Philippines
| | - Tapas Kumer Hore
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, College, Laguna, Philippines
- Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - Alvin D Palanog
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños (UPLB), 4031, College, Laguna, Philippines
- PhilRice Negros, Philippine Rice Research Institute, Murcia, Negros, Philippines
| | - Amery Amparado
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Mary Ann Inabangan-Asilo
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Gaurav Joshi
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - Balachiranjeevi Chintavaram
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
| | - B P Mallikarjuna Swamy
- Rice Breeding and Innovation Department, International Rice Research Institute, DAPO 7777, Metro Manila, Philippines.
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2
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Naveenkumar R, Anandan A, Prabhukarthikeyan SR, Mahender A, Sangeetha G, Vaish SS, Singh PK, Hussain W, Ali J. Dissecting genomic regions and underlying sheath blight resistance traits in rice ( Oryza sativa L.) using a genome-wide association study. PLANT DIRECT 2023; 7:e540. [PMID: 38028647 PMCID: PMC10667636 DOI: 10.1002/pld3.540] [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: 05/23/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023]
Abstract
The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome-wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro-morphological and disease-resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker-trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.
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Affiliation(s)
- R Naveenkumar
- Crop Improvement DivisionICAR‐National Rice Research Institute (NRRI)CuttackOdishaIndia
- Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar PradeshIndia
- Division of Plant Pathology, School of Agricultural SciencesKarunya Institute of Technology and SciencesCoimbatoreTamil NaduIndia
| | - Annamalai Anandan
- Crop Improvement DivisionICAR‐National Rice Research Institute (NRRI)CuttackOdishaIndia
- ICAR‐Indian Institute of Seed ScienceBangaloreKarnatakaIndia
| | | | - Anumalla Mahender
- Rice Breeding Innovation PlatformInternational Rice Research Institute (IRRI)Los BañosLagunaPhilippines
| | - Ganesan Sangeetha
- Division of Crop ProtectionICAR‐Indian Institute of Horticultural ResearchBangaloreKarnatakaIndia
| | - Shyam Saran Vaish
- Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar PradeshIndia
| | - Pawan Kumar Singh
- Institute of Agricultural SciencesBanaras Hindu UniversityVaranasiUttar PradeshIndia
| | - Waseem Hussain
- Rice Breeding Innovation PlatformInternational Rice Research Institute (IRRI)Los BañosLagunaPhilippines
| | - Jauhar Ali
- Rice Breeding Innovation PlatformInternational Rice Research Institute (IRRI)Los BañosLagunaPhilippines
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Barik SR, Moharana A, Pandit E, Behera A, Mishra A, Mohanty SP, Mohapatra S, Sanghamitra P, Meher J, Pani DR, Bhadana VP, Datt S, Sahoo CR, Raj K R R, Pradhan SK. Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches. Int J Mol Sci 2023; 24:10708. [PMID: 37445885 DOI: 10.3390/ijms241310708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 07/15/2023] Open
Abstract
Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC1F1, BC2F1, and BC3F1 generation, respectively. Recurrent parent's genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC3F2 progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.
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Affiliation(s)
| | - Arpita Moharana
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Elssa Pandit
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, India
| | | | - Ankita Mishra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | | | - Shibani Mohapatra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | | | | | - Dipti Ranjan Pani
- ICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, India
| | - Vijai Pal Bhadana
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834003, India
| | - Shiv Datt
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
| | - Chita Ranjan Sahoo
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Reshmi Raj K R
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
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4
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Senguttuvel P, G P, C J, D SR, CN N, V J, P B, R G, J AK, SV SP, LV SR, AS H, K S, D S, RM S, Govindaraj M. Rice biofortification: breeding and genomic approaches for genetic enhancement of grain zinc and iron contents. FRONTIERS IN PLANT SCIENCE 2023; 14:1138408. [PMID: 37332714 PMCID: PMC10272457 DOI: 10.3389/fpls.2023.1138408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/25/2023] [Indexed: 06/20/2023]
Abstract
Rice is a highly consumed staple cereal cultivated predominantly in Asian countries, which share 90% of global rice production. Rice is a primary calorie provider for more than 3.5 billion people across the world. Preference and consumption of polished rice have increased manifold, which resulted in the loss of inherent nutrition. The prevalence of micronutrient deficiencies (Zn and Fe) are major human health challenges in the 21st century. Biofortification of staples is a sustainable approach to alleviating malnutrition. Globally, significant progress has been made in rice for enhancing grain Zn, Fe, and protein. To date, 37 biofortified Fe, Zn, Protein and Provitamin A rich rice varieties are available for commercial cultivation (16 from India and 21 from the rest of the world; Fe > 10 mg/kg, Zn > 24 mg/kg, protein > 10% in polished rice as India target while Zn > 28 mg/kg in polished rice as international target). However, understanding the micronutrient genetics, mechanisms of uptake, translocation, and bioavailability are the prime areas that need to be strengthened. The successful development of these lines through integrated-genomic technologies can accelerate deployment and scaling in future breeding programs to address the key challenges of malnutrition and hidden hunger.
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Affiliation(s)
- P. Senguttuvel
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Padmavathi G
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Jasmine C
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
- Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Sanjeeva Rao D
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Neeraja CN
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Jaldhani V
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Beulah P
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Gobinath R
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Aravind Kumar J
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Sai Prasad SV
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Subba Rao LV
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Hariprasad AS
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Sruthi K
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Shivani D
- Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Sundaram RM
- Crop Improvement Section, ICAR - Indian Institute of Rice Research (ICAR - IIRR), Hyderabad, India
| | - Mahalingam Govindaraj
- HarvestPlus, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Mohanty SP, Nayak DK, Sanghamitra P, Barik SR, Pandit E, Behera A, Pani DR, Mohapatra S, Raj K R R, Pradhan KC, Sahoo CR, Mohanty MR, Behera C, Panda AK, Jena BK, Behera L, Dash PK, Pradhan SK. Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice. Genes (Basel) 2023; 14:genes14040902. [PMID: 37107660 PMCID: PMC10138111 DOI: 10.3390/genes14040902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker-trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.
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Affiliation(s)
| | | | | | | | - Elssa Pandit
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, India
| | | | - Dipti Ranjan Pani
- ICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, India
| | - Shibani Mohapatra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Reshmi Raj K R
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kartik Chandra Pradhan
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Chita Ranjan Sahoo
- Directorate of Research, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Mihir Ranjan Mohanty
- Regional Research and Technology Transfer Station (RRTTS), Odisha University of Agriculture & Technology, Jeypore 764001, India
| | - Chinmayee Behera
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, SOA University, Bhubaneswar 753001, India
| | - Alok Kumar Panda
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Binod Kumar Jena
- Krishi Vigyan Kendra, Odisha University of Agriculture & Technology, Rayagada 765022, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110012, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
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6
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Palanog AD, Nha CT, Descalsota-Empleo GIL, Calayugan MI, Swe ZM, Amparado A, Inabangan-Asilo MA, Hernandez JE, Sta. Cruz PC, Borromeo TH, Lalusin AG, Mauleon R, McNally KL, Swamy BPM. Molecular dissection of connected rice populations revealed important genomic regions for agronomic and biofortification traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1157507. [PMID: 37035067 PMCID: PMC10073715 DOI: 10.3389/fpls.2023.1157507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Breeding staple crops with increased micronutrient concentration is a sustainable approach to address micronutrient malnutrition. We carried out Multi-Cross QTL analysis and Inclusive Composite Interval Mapping for 11 agronomic, yield and biofortification traits using four connected RILs populations of rice. Overall, MC-156 QTLs were detected for agronomic (115) and biofortification (41) traits, which were higher in number but smaller in effects compared to single population analysis. The MC-QTL analysis was able to detect important QTLs viz: qZn5.2, qFe7.1, qGY10.1, qDF7.1, qPH1.1, qNT4.1, qPT4.1, qPL1.2, qTGW5.1, qGL3.1 , and qGW6.1 , which can be used in rice genomics assisted breeding. A major QTL (qZn5.2 ) for grain Zn concentration has been detected on chromosome 5 that accounted for 13% of R2. In all, 26 QTL clusters were identified on different chromosomes. qPH6.1 epistatically interacted with qZn5.1 and qGY6.2 . Most of QTLs were co-located with functionally related candidate genes indicating the accuracy of QTL mapping. The genomic region of qZn5.2 was co-located with putative genes such as OsZIP5, OsZIP9, and LOC_OS05G40490 that are involved in Zn uptake. These genes included polymorphic functional SNPs, and their promoter regions were enriched with cis-regulatory elements involved in plant growth and development, and biotic and abiotic stress tolerance. Major effect QTL identified for biofortification and agronomic traits can be utilized in breeding for Zn biofortified rice varieties.
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Affiliation(s)
- Alvin D. Palanog
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
- PhilRice Negros Branch Station, Philippine Rice Research Institute, Murcia, Negros Occidental, Philippines
| | | | | | - Mark Ian Calayugan
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Zin Mar Swe
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Amery Amparado
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Mary Ann Inabangan-Asilo
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Jose E. Hernandez
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Pompe C. Sta. Cruz
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Teresita H. Borromeo
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Antonio G. Lalusin
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Laguna, Philippines
| | - Ramil Mauleon
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
- College of Agriculture, University of Southern Mindanao, Kabacan, North Cotabato, Philippines
| | - Kenneth L. McNally
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - B. P. Mallikarjuna Swamy
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
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Mohapatra S, Barik SR, Dash PK, Lenka D, Pradhan KC, Raj K. R R, Mohanty SP, Mohanty MR, Sahoo A, Jena BK, Panda AK, Panigrahi D, Dash SK, Meher J, Sahoo CR, Mukherjee AK, Das L, Behera L, Pradhan SK. Molecular Breeding for Incorporation of Submergence Tolerance and Durable Bacterial Blight Resistance into the Popular Rice Variety 'Ranidhan'. Biomolecules 2023; 13:biom13020198. [PMID: 36830568 PMCID: PMC9953461 DOI: 10.3390/biom13020198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety is susceptible to the disease. BB resistance genes Xa21, xa13, and xa5, along with the Sub1 QTL, for submergence stress tolerance were transferred into the variety using marker-assisted backcross breeding approach. Foreground selection using direct and closely linked markers detected the progenies carrying all four target genes in the BC1F1, BC2F1, and BC3F1 generations, and the positive progenies carrying these genes with maximum similarity to the recipient parent, Ranidhan, were backcrossed into each segregating generation. Foreground selection in the BC1F1 generation progenies detected all target genes in 11 progenies. The progeny carrying all target genes and similar to the recipient parent in terms of phenotype was backcrossed, and a total of 321 BC2F1 seeds were produced. Ten progenies carried all target genes/QTL in the BC2F1 generation. Screening of the BC3F1 progenies using markers detected 12 plants carrying the target genes. A total of 1270 BC3F2 seeds were obtained from the best BC3F1 progeny. Foreground selection in the BC3F2 progenies detected four plants carrying the target genes in the homozygous condition. The bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight pathogen. These BB pyramided lines were submergence-tolerant and similar to Ranidhan in 13 agro-morphologic and grain quality traits; hence, they are likely to be adopted by farmers.
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Affiliation(s)
- Shibani Mohapatra
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | | | - Prasanta K. Dash
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Devidutta Lenka
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Kartika Chandra Pradhan
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | - Reshmi Raj K. R
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | | | | | - Ambika Sahoo
- Centre for Biotechnology, Siksha ‘O’ Anusandhan Deemed to be University, Bhubaneswar 751003, India
| | | | - Alok Kumar Panda
- Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India
| | - Debabrata Panigrahi
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | | | | | - Chitta Ranjan Sahoo
- College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India
| | | | - Lipi Das
- ICAR-Central Institute for Women in Agriculture, Bhubaneswar 751003, India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India
- Correspondence:
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8
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Nayak DK, Sahoo S, Barik SR, Sanghamitra P, Sangeeta S, Pandit E, Reshmi Raj KR, Basak N, Pradhan SK. Association mapping for protein, total soluble sugars, starch, amylose and chlorophyll content in rice. BMC PLANT BIOLOGY 2022; 22:620. [PMID: 36581797 PMCID: PMC9801606 DOI: 10.1186/s12870-022-04015-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/21/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Protein, starch, amylose and total soluble sugars are basic metabolites of seed that influence the eating, cooking and nutritional qualities of rice. Chlorophyll is responsible for the absorption and utilization of the light energy influencing photosynthetic efficiency in rice plant. Mapping of these traits are very important for detection of more number of robust markers for improvement of these traits through molecular breeding approaches. RESULTS A representative panel population was developed by including 120 germplasm lines from the initial shortlisted 274 lines for mapping of the six biochemical traits using 136 microsatellite markers through association mapping. A wide genetic variation was detected for the traits, total protein, starch, amylose, total soluble sugars, chlorophyll a, and chlorophyll b content in the population. Specific allele frequency, gene diversity, informative markers and other diversity parameters obtained from the population indicated the effectiveness of utilization of the population and markers for mapping of these traits. The fixation indices values estimated from the population indicated the existence of linkage disequilibrium for the six traits. The population genetic structure at K = 3 showed correspondence with majority of the members in each group for the six traits. The reported QTL, qProt1, qPC6.2, and qPC8.2 for protein content; qTSS8.1 for total soluble sugar; qAC1.2 for amylose content; qCH2 and qSLCHH for chlorophyll a (Chl. a) while qChl5D for chlorophyll b (Chl. b) were validated in this population. The QTL controlling total protein content qPC1.2; qTSS7.1, qTSS8.2 and qTSS12.1 for total soluble sugars; qSC2.1, qSC2.2, qSC6.1 and qSC11.1 for starch content; qAC11.1, qAC11.2 and qAC11.3 for amylose content; qChla8.1 for Chl. a content and qChlb7.1 and qChlb8.1 for Chl. b identified by both Generalized Linear Model and Mixed Linear Model were detected as novel QTL. The chromosomal regions on chromosome 8 at 234 cM for grain protein content and total soluble sugars and at 363 cM for Chl. a and Chl. b along with the position at 48 cM on chromosome 11 for starch and amylose content are genetic hot spots for these traits. CONCLUSION The validated, co-localized and the novel QTL detected in this study will be useful for improvement of protein, starch, amylose, total soluble sugars and chlorophyll content in rice.
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Affiliation(s)
- D K Nayak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S Sahoo
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
- College of Agriculture, OUAT, Bhabaneswar, Odisha, 751003, India
| | - S R Barik
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - P Sanghamitra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S Sangeeta
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - E Pandit
- Fakir Mohan University, Balasore, Odisha, 756020, India
| | - K R Reshmi Raj
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - N Basak
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - S K Pradhan
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
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Uttam GA, Suman K, Jaldhani V, Babu PM, Rao DS, Sundaram RM, Neeraja CN. Identification of Genomic Regions Associated with High Grain Zn Content in Polished Rice Using Genotyping-by-Sequencing (GBS). PLANTS (BASEL, SWITZERLAND) 2022; 12:144. [PMID: 36616273 PMCID: PMC9824299 DOI: 10.3390/plants12010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Globally, micronutrient (iron and zinc) enriched rice has been a sustainable and cost-effective solution to overcome malnutrition or hidden hunger. Understanding the genetic basis and identifying the genomic regions for grain zinc (Zn) across diverse genetic backgrounds is an important step to develop biofortified rice varieties. In this case, an RIL population (306 RILs) obtained from a cross between the high-yielding rice variety MTU1010 and the high-zinc rice variety Ranbir Basmati was utilized to pinpoint the genomic region(s) and QTL(s) responsible for grain zinc (Zn) content. A total of 2746 SNP markers spanning a genetic distance of 2445 cM were employed for quantitative trait loci (QTL) analysis, which resulted in the identification of 47 QTLs for mineral (Zn and Fe) and agronomic traits with 3.5-36.0% phenotypic variance explained (PVE) over the seasons. On Chr02, consistent QTLs for grain Zn polished (qZnPR.2.1) and Zn brown (qZnBR.2.2) were identified. On Chr09, two additional reliable QTLs for grain Zn brown (qZnBR.9.1 and qZnBR.9.2) were identified. The major-effect QTLs identified in this study were associated with few key genes related to Zn and Fe transporter activity. The genomic regions, candidate genes, and molecular markers associated with these major QTLs will be useful for genomic-assisted breeding for developing Zn-biofortified varieties.
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10
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Naveenkumar R, Anandan A, Singh V, Prabhukarthikeyan S, Parameswaran C, Sangeetha G, Mahender A, Keerthana U, Singh P, Patra B, Ali J. Deciphering environmental factors and defense response of rice genotypes against sheath blight disease. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2022; 122:101916. [PMID: 36405863 PMCID: PMC9669783 DOI: 10.1016/j.pmpp.2022.101916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Sheath blight (ShB) is one of the most serious diseases in rice, leading to severe yield losses globally. In our study, we evaluated a total of 63 rice genotypes for resistance against sheath blight disease by artificial inoculation over two seasons under field conditions and studied the weather parameters associated with disease incidence. Based on two years of testing, 23 genotypes were found moderately resistant, 38 were moderately susceptible, and 2 exhibited a susceptible reaction to sheath blight disease. Among the specific four genotypes (IC283139, IC283041, IC283038, and IC283023) of the moderately resistant group exhibited less disease reaction in comparison with check variety Tetep. Further, the correlation of percent disease index (PDI) with weather parameters revealed negative associations between PDI and maximum temperature, minimum temperature, low rainfall and the positive association with maximum relative humidity (RH) suggest that very low temperature or high precipitation might have a negative impact on pathogen establishment. In addition, the sheath blight-linked SSRs were assessed using distance and model-based approaches, results of both the models revealed that genotypes distinguished the resistant population from the susceptible one. From the output of two years of principal component analysis, two genotypes from each group of moderately resistant, moderately susceptible and susceptible were studied for their biochemical reaction against the sheath blight pathogen. The biochemical study revealed that the accumulation of defense and antioxidant enzymes, namely, polyphenol oxidase, peroxidase, total phenol, phenylalanine ammonia-lyase, catalase, and superoxide dismutase, were higher in moderately resistant genotypes, but was observed to be lower in moderately susceptible and susceptible genotypes. The statistical analysis revealed the enzyme activities (defense and antioxidant) exhibited a strong negative correlation with area under the disease progress curve (AUDPC) and influence of weather parameter RH. This demonstrates that the environment factor RH plays a major role in imparting the resistance mechanism by decreasing the enzymes activities and increasing PDI. This study found that the identified novel resistant genotype (IC283139) with purple stem base demonstrated improved resistance against sheath blight infection through a defense response and the use of antioxidant machinery.
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Affiliation(s)
- R. Naveenkumar
- Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
- Institute of Agricultural Sciences, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
- Department of Agriculture, Karunya Institute of Technology and Sciences, Karunya Nagar, Coimbatore, Tamil Nadu, 641114, India
| | - A. Anandan
- Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
- ICAR-Indian Institute of Seed Science, Regional Station, Bangalore, 560065, Karnataka, India
| | - Vineeta Singh
- Institute of Agricultural Sciences, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - S.R. Prabhukarthikeyan
- Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - C. Parameswaran
- Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - G. Sangeetha
- ICAR-Indian Institute of Horticultural Research (IIHR), Bangalore, 560089, Karnataka, India
| | - A. Mahender
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Laguna, 4031, Philippines
| | - U. Keerthana
- Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - P.K. Singh
- Institute of Agricultural Sciences, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - B.C. Patra
- Indian Council of Agricultural Research (ICAR)-National Rice Research Institute (NRRI), Cuttack, Odisha, 753006, India
| | - Jauhar Ali
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Laguna, 4031, Philippines
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11
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Viana VE, Maltzahn LE, Costa de Oliveira A, Pegoraro C. Genetic Approaches for Iron and Zinc Biofortification and Arsenic Decrease in Oryza sativa L. Grains. Biol Trace Elem Res 2022; 200:4505-4523. [PMID: 34773578 DOI: 10.1007/s12011-021-03018-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/04/2021] [Indexed: 12/29/2022]
Abstract
Rice is the staple diet to half of the world's population, being a major source of carbohydrates, vitamins, and some essential elements. However, rice naturally contains low amounts of essential minerals such as iron (Fe) and zinc (Zn), which are drastically decreased after milling. Thus, populations that consume mostly rice may have micronutrient deficiency, which is associated with different diseases. On the other hand, rice irrigated by flooding has a high ability to accumulate arsenic (As) in the grain. Therefore, when rice is grown in areas with contaminated soil or irrigation water, it represents a risk factor for consumers, since As is associated with cancer and other diseases. Different strategies have been used to mitigate micronutrient deficiencies such as Fe and Zn and to prevent As from entering the food chain. Each strategy has its positive and its negative sides. The development of genetically biofortified rice plants with Fe and Zn and with low As accumulation is one of the most promising strategies, since it does not represent an additional cost for farmers, and gives benefits to consumers as well. Considering the importance of genetic improvement (traditional or molecular) to decrease the impact of micronutrient deficiencies such as Fe and Zn and contamination with As, this review aimed to summarize the major efforts, advances, and challenges for genetic biofortification of Fe and Zn and decrease in As content in rice grains.
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Affiliation(s)
- Vívian Ebeling Viana
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Latóia Eduarda Maltzahn
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil
| | - Camila Pegoraro
- Centro de Genômica E Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão Do Leão, Brazil.
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12
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Zulfiqar A, Naseer S, Saleem A, Ahmed S, Sardar R. Genetic diversity studies for grain iron and zinc content analysis for Elite rice (Oryza sativa L.) genotype by using SSR markers. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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13
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Unraveling the genomic regions controlling the seed vigour index, root growth parameters and germination per cent in rice. PLoS One 2022; 17:e0267303. [PMID: 35881571 PMCID: PMC9321372 DOI: 10.1371/journal.pone.0267303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/06/2022] [Indexed: 12/21/2022] Open
Abstract
High seed vigour ensures good quality seed and higher productivity. Early seedling growth parameters indicate seed vigour in rice. Seed vigour via physiological growth parameters is a complex trait controlled by many quantitative trait loci. A panel was prepared representing a population of 274 rice landraces by including genotypes from all the phenotypic groups of sixseedling stage physiological parameters including germination % for association mapping. Wide variations for the six studiedtraits were observed in the population. The population was classified into 3 genetic groups. Fixation indices indicated the presence of linkage disequilibrium in the population. The population was classified into subpopulations and each subpopulation showed correspondence with the 6 physiological traits. A total of 5 reported QTLs viz., qGP8.1 for germination % (GP); qSVII2.1, qSVII6.1 and qSVII6.2 for seed vigour index II (SVII), and qRSR11.1 for root-shoot ratio (RSR) were validated in this mapping population. In addition, 13 QTLs regulating the physiological parameters such as qSVI 11.1 for seed vigour index I; qSVI11.1 and qSVI12.1 for seed vigour index II; qRRG10.1, qRRG8.1, qRRG8.2, qRRG6.1 and qRRG4.1 for rate of root growth (RRG); qRSR2.1, qRSR3.1 and qRSR5.1 for root-shoot ratio (RSR) while qGP6.2 and qGP6.3 for germination %were identified. Additionally, co-localization or co-inheritance of QTLs, qGP8.1 and qSVI8.1 for GP and SVI-1; qGP6.2 and qRRG6.1 for GP and RRG, and qSVI11.1 and qRSR11.1 for SVI and RSR were detected. The QTLs identified in this study will be useful for improvement of seed vigour trait in rice.
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14
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Han M, Zhang J, Li D, Sun S, Zhang C, Zhang C, Yan L, Guan Y, Chen L, Guo Y, You M, Gou W, Li X, Yan J, Bai S, Yan X. Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:882601. [PMID: 35845670 PMCID: PMC9277506 DOI: 10.3389/fpls.2022.882601] [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: 02/25/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Elymus sibiricus L. is a perennial allotetraploid belonging to Triticeae of Poaceae, Elymus L., as the type species of genus Elymus L. The existing geographical distribution pattern and genetic spatial structure of E. sibiricus on Qinghai-Tibetan Plateau (QTP) are not yet clear. In this study, population genetic structure and demography history of 216 individuals from 44 E. sibiricus populations on QTP were studied used specific-locus amplified fragment sequencing (SLAF-seq). The result of genetic diversity showed that there was no single genetic diversity center was observed across all E. sibiricus populations. The results of genetic variation showed that 44 populations were clearly divided into the following three groups: Qinghai Plateau (Group I), South Tibet (Group II), and Hengduan Mountains (Group III). From the three analyses of AMOVA, Mantel test and Treemix, strong genetic differentiation across all populations and low genetic differentiation among populations within three groups. Molecular dating indicated that E. sibiricus diverged at 16.08 Ma (during the early Miocene) can be linked to the Himalayan Motion stage of QTP uplift. It is speculated that the reasons affecting the current phylogeographical pattern are as follows: (1) The environmental changes due to the uplift of the QTP; (2) The geographic distance between the populations (Groups I and III are close in geographic distance, and gene flow are frequent); (3) Geographical barriers (the Tanggula and Bayangela Mountains between Groups I and II). This study provides new evidence and historical perspective to the future exploration of the evolution and geographic distribution pattern of Elymus L.
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Affiliation(s)
- Mengli Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingxue Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Daxu Li
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Shengnan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lijun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yongzhuo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Lili Chen
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yuxia Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Minghong You
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xinrui Li
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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15
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Kong D, Khan SA, Wu H, Liu Y, Ling HQ. Biofortification of iron and zinc in rice and wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1157-1167. [PMID: 35396901 DOI: 10.1111/jipb.13262] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
Iron and zinc are critical micronutrients for human health. Approximately two billion people suffer from iron and zinc deficiencies worldwide, most of whom rely on rice (Oryza sativa) and wheat (Triticum aestivum) as staple foods. Therefore, biofortifying rice and wheat with iron and zinc is an important and economical approach to ameliorate these nutritional deficiencies. In this review, we provide a brief introduction to iron and zinc uptake, translocation, storage, and signaling pathways in rice and wheat. We then discuss current progress in efforts to biofortify rice and wheat with iron and zinc. Finally, we provide future perspectives for the biofortification of rice and wheat with iron and zinc.
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Affiliation(s)
- Danyu Kong
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Sabaz Ali Khan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- Department of Biotechnology, COMSATS University Islamabad-Abbottabad Campus, University Road, Abbottabad, 22060, Pakistan
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Sanghamitra P, Barik SR, Bastia R, Mohanty SP, Pandit E, Behera A, Mishra J, Kumar G, Pradhan SK. Detection of Genomic Regions Controlling the Antioxidant Enzymes, Phenolic Content, and Antioxidant Activities in Rice Grain through Association Mapping. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111463. [PMID: 35684236 PMCID: PMC9183076 DOI: 10.3390/plants11111463] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 05/08/2023]
Abstract
Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice.
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Affiliation(s)
- Priyadarsini Sanghamitra
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Saumya Ranjan Barik
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Ramakrushna Bastia
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Shakti Prakash Mohanty
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Elssa Pandit
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, Odisha, India
| | - Abhisarika Behera
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Jyotirmayee Mishra
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Gaurav Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India; (P.S.); (S.R.B.); (R.B.); (S.P.M.); (E.P.); (A.B.); (J.M.); (G.K.)
- Correspondence:
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17
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Thabet SG, Alomari DZ, Brinch-Pedersen H, Alqudah AM. Genetic analysis toward more nutritious barley grains for a food secure world. BOTANICAL STUDIES 2022; 63:6. [PMID: 35267113 PMCID: PMC8913823 DOI: 10.1186/s40529-022-00334-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Understanding the relationships between nutrition, human health and plant food source is among the highest priorities for public health. Therefore, enhancing the minerals content such as iron (Fe), zinc (Zn) and selenium (Se) in barley (Hordeum vulgare L.) grains is an urgent need to improve the nutritive value of barley grains in overcoming malnutrition and its potential consequencing. This study aimed to expedite biofortification of barley grains by elucidating the genetic basis of Zn, Fe, and Se accumulation in the grains, which will contribute to improved barley nutritional quality. RESULTS A genome-wide association study (GWAS) was conducted to detect the genetic architecture for grain Zn, Fe, and Se accumulations in 216 spring barley accessions across two years. All the accessions were genotyped by single nucleotide polymorphisms (SNPs) molecular markers. Mineral heritability values ranging from moderate to high were revealed in both environments. Remarkably, there was a high natural phenotypic variation for all micronutrient accumulation in the used population. High-LD SNP markers (222 SNPs) were detected to be associated with all micronutrients in barley grains across the two environments plus BLUEs. Three genomic regions were detected based on LD, which were identified for the most effective markers that had associations with more than one trait. The strongest SNP-trait associations were found to be physically located within genes that may be involved in grain Zn and Fe homeostasis. Two putative candidate genes were annotated as Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively, and have been suggested as candidates for increased grain Zn, Fe, and Se accumulation. CONCLUSIONS These findings shed a light on the genetic basis of Zn, Fe, and Se accumulation in barley grains and have the potential to assist plant breeders in selecting accessions with high micronutrient concentrations to enhance grain quality and, ultimately human health.
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Affiliation(s)
- Samar G Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt.
| | - Dalia Z Alomari
- Department of Agroecology, Aarhus University, 4200, Flakkebjerg, Slagelse, Denmark
| | | | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University, 4200, Flakkebjerg, Slagelse, Denmark.
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Stanton C, Sanders D, Krämer U, Podar D. Zinc in plants: Integrating homeostasis and biofortification. MOLECULAR PLANT 2022; 15:65-85. [PMID: 34952215 DOI: 10.1016/j.molp.2021.12.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 05/24/2023]
Abstract
Zinc plays many essential roles in life. As a strong Lewis acid that lacks redox activity under environmental and cellular conditions, the Zn2+ cation is central in determining protein structure and catalytic function of nearly 10% of most eukaryotic proteomes. While specific functions of zinc have been elucidated at a molecular level in a number of plant proteins, wider issues abound with respect to the acquisition and distribution of zinc by plants. An important challenge is to understand how plants balance between Zn supply in soil and their own nutritional requirement for zinc, particularly where edaphic factors lead to a lack of bioavailable zinc or, conversely, an excess of zinc that bears a major risk of phytotoxicity. Plants are the ultimate source of zinc in the human diet, and human Zn deficiency accounts for over 400 000 deaths annually. Here, we review the current understanding of zinc homeostasis in plants from the molecular and physiological perspectives. We provide an overview of approaches pursued so far in Zn biofortification of crops. Finally, we outline a "push-pull" model of zinc nutrition in plants as a simplifying concept. In summary, this review discusses avenues that can potentially deliver wider benefits for both plant and human Zn nutrition.
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Affiliation(s)
| | - Dale Sanders
- John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Dorina Podar
- Department of Molecular Biology and Biotechnology and Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400084 Cluj-Napoca, Romania.
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Beena R, Kirubakaran S, Nithya N, Manickavelu A, Sah RP, Abida PS, Sreekumar J, Jaslam PM, Rejeth R, Jayalekshmy VG, Roy S, Manju RV, Viji MM, Siddique KHM. Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces. BMC PLANT BIOLOGY 2021; 21:484. [PMID: 34686134 PMCID: PMC8539776 DOI: 10.1186/s12870-021-03272-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/29/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. RESULTS Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. CONCLUSION The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.
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Affiliation(s)
- Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | | | - Narayanan Nithya
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Alagu Manickavelu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala India
| | - Rameshwar Prasad Sah
- Indian Council of Agricultural Research (ICAR)-Central Rice Research Institute, currently named National Rice Research Institute (NRRI), Cuttack, Odisha India
| | - Puthenpeedikal Salim Abida
- Regional Agricultural Research Station, Pattambi, Kerala Agricultural University, Palakkad, Kerala India
| | - Janardanan Sreekumar
- Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram, Kerala India
| | | | - Rajendrakumar Rejeth
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Vijayalayam Gengamma Jayalekshmy
- Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Stephen Roy
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Ramakrishnan Vimala Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Mariasoosai Mary Viji
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
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20
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Talukdar P, Travis AJ, Hossain M, Islam MR, Norton GJ, Price AH. Identification of genomic loci regulating grain iron content in
aus
rice under two irrigation management systems. Food Energy Secur 2021; 11:e329. [PMID: 35866052 PMCID: PMC9286631 DOI: 10.1002/fes3.329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/15/2022] Open
Abstract
Iron (Fe) deficiency is one of the common causes of anaemia in humans. Improving grain Fe in rice, therefore, could have a positive impact for humans worldwide, especially for those people who consume rice as a staple food. In this study, 225–269 accessions of the Bengal and Assam Aus Panel (BAAP) were investigated for their accumulation of grain Fe in two consecutive years in a field experiment under alternative wetting and drying (AWD) and continuous flooded (CF) irrigation. AWD reduced straw Fe by 40% and grain Fe by 5.5–13%. Genotype differences accounted for 35% of the variation in grain Fe, while genotype by irrigation interaction accounted for 12% of the variation in straw and grain Fe in year 1, with no significant interactions detected in year 2. Twelve rice accessions were identified as having high grain Fe for both years regardless of irrigation treatment, half of which were from BAAP aus subgroup 3 which prominently comes from Bangladesh. On average, subgroup 3 had higher grain Fe than the other four subgroups of aus. Genome‐wide association mapping identified 6 genomic loci controlling natural variation of grain Fe concentration in plants grown under AWD. For one QTL, nicotianamine synthase OsNAS3 is proposed as candidate for controlling natural variation of grain Fe in rice. The BAAP contains three haplotypes of OsNAS3 where one haplotype (detected in 31% of the individuals) increased grain Fe up to 11%. Haplotype analysis of this gene in rice suggests that the ability to detect the QTL is enhanced in the BAAP because the high Fe allele is balanced in aus, unlike indica and japonica subgroups.
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Affiliation(s)
- Partha Talukdar
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | | | - Mahmud Hossain
- Department of Soil Science Bangladesh Agricultural University Mymensingh Bangladesh
| | - Md Rafiqul Islam
- Department of Soil Science Bangladesh Agricultural University Mymensingh Bangladesh
| | - Gareth J. Norton
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Adam H. Price
- School of Biological Sciences University of Aberdeen Aberdeen UK
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21
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de Oliveira VF, Busanello C, Viana VE, Stafen CF, Pedrolo AM, Paniz FP, Pedron T, Pereira RM, Rosa SA, de Magalhães Junior AM, Costa de Oliveira A, Batista BL, Pegoraro C. Assessing mineral and toxic elements content in rice grains grown in southern Brazil. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Pawar S, Pandit E, Mohanty IC, Saha D, Pradhan SK. Population genetic structure and association mapping for iron toxicity tolerance in rice. PLoS One 2021; 16:e0246232. [PMID: 33647046 PMCID: PMC7920388 DOI: 10.1371/journal.pone.0246232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 11/11/2020] [Indexed: 02/01/2023] Open
Abstract
Iron (Fe) toxicity is a major abiotic stress which severely reduces rice yield in many countries of the world. Genetic variation for this stress tolerance exists in rice germplasms. Mapping of gene(s)/QTL controlling the stress tolerance and transfer of the traits into high yielding rice varieties are essential for improvement against the stress. A panel population of 119 genotypes from 352 germplasm lines was constituted for detecting the candidate gene(s)/QTL through association mapping. STRUCTURE, GenAlEx and Darwin softwares were used to classify the population. The marker-trait association was detected by considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) analyses. Wide genetic variation was observed among the genotypes present in the panel population for the stress tolerance. Linkage disequilibrium was detected in the population for iron toxicity tolerance. The population was categorized into three genetic structure groups. Marker-trait association study considering both the Generalized Linear Model (GLM) and Mixed Linear Model (MLM) showed significant association of leaf browning index (LBI) with markers RM471, RM3, RM590 and RM243. Three novel QTL controlling Fe-toxicity tolerance were detected and designated as qFeTox4.3, qFeTox6.1 and qFeTox10.1. A QTL reported earlier in the marker interval of C955-C885 on chromosome 1 is validated using this panel population. The present study showed that QTL controlling Fe-toxicity tolerance to be co-localized with the QTL for Fe-biofortification of rice grain indicating involvement of common pathway for Fe toxicity tolerance and Fe content in rice grain. Fe-toxicity tolerance QTL qFeTox6.1 was co-localized with grain Fe-biofortification QTLs qFe6.1 and qFe6.2 on chromosome 6, whereas qFeTox10.1 was co-localized with qFe10.1 on chromosome 10. The Fe-toxicity tolerance QTL detected from this mapping study will be useful in marker-assisted breeding programs.
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Affiliation(s)
- S. Pawar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - E. Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
- Department of Bio-Science and Bio-Technology, Fakir Mohan University, Balasore, Odisha, India
| | - I. C. Mohanty
- Department of Biotechnology, College of Agriculture, OUAT, Bhubaneswar, Odisha, India
| | - D. Saha
- Department of Biotechnology, College of Agriculture, OUAT, Bhubaneswar, Odisha, India
| | - S. K. Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India
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Mohapatra S, Panda AK, Bastia AK, Mukherjee AK, Sanghamitra P, Meher J, Mohanty SP, Pradhan SK. Development of Submergence-Tolerant, Bacterial Blight-Resistant, and High-Yielding Near Isogenic Lines of Popular Variety, 'Swarna' Through Marker-Assisted Breeding Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:672618. [PMID: 34386025 PMCID: PMC8353458 DOI: 10.3389/fpls.2021.672618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 05/13/2023]
Abstract
The rice variety 'Swarna' is highly popular in the eastern region of India. The farmers of eastern India cultivate mainly rainfed rice and face the adverse effects of climate change very frequently. Rice production in this region is not stable. Swarna variety is highly susceptible to bacterial blight (BB) disease and flash floods, which cause a heavy reduction in the yield. Transfer of five target genes/QTLs was targeted into the variety, Swarna by adopting marker-assisted backcross breeding approach. Direct markers for Sub1A, OsSPL14, and SCM2 QTLs and closely linked markers for xa5 and Xa21 BB resistance genes were screened in the backcross progenies. Swarna-Sub1, CR Dhan 800, and Swarna-Habataki near-isogenic lines (NILs) were used as donor parents in the breeding program. True multiple F1 plants were identified for backcrossing, and 796 BC1F1 seeds were generated. Foreground selection detected all the five target genes in six progenies in BC1F1 generation. The progeny containing all the target genes and more similar with the recipient parent was backcrossed, and a total of 446 BC2F1 seeds were produced. Foreground screening detected four BC2F1 plants carrying the five target genes. A total of 2,145 BC2F2 seeds were obtained from the best BC2F1 progeny. Screening of the progenies resulted in one plant with all five desirable genes, three plants with four, and another three progenies carrying three genes in homozygous conditions. The pyramided lines showed higher BB resistance and submergence tolerance than the recipient parent, Swarna. Culm strength of the pyramided lines showed higher breaking force than the recipient parent, Swarna. The pyramided line, SSBY-16-68-69 yielded the highest grain yield of 7.52 t/ha followed by the lines SSBY-16-68-511 (7.34 t/ha) and SSBY-16-68-1633 (7.02 t/ha). The best-pyramided line showed a yield advantage of 18% over the recipient parent and 6.8% over the yield component donor parent. Seven pyramided lines showed higher yield than the recipient parent, while five lines were better yielders than the yield component donor parent. The pyramided line SSBY-16-68-69 produced 365 grains/panicle, while the recipient had 152. The main morphologic and grain quality features of the recipient parent were retained in the pyramided lines.
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Affiliation(s)
| | - Alok Kumar Panda
- School of Applied Sciences, KIIT Deemed to Be University, Bhubaneswar, India
| | | | | | | | | | | | - Sharat Kumar Pradhan
- ICAR—National Rice Research Institute, Cuttack, India
- *Correspondence: Sharat Kumar Pradhan
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24
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Suman K, Neeraja CN, Madhubabu P, Rathod S, Bej S, Jadhav KP, Kumar JA, Chaitanya U, Pawar SC, Rani SH, Subbarao LV, Voleti SR. Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2021; 12:587482. [PMID: 33679823 PMCID: PMC7930840 DOI: 10.3389/fpls.2021.587482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/06/2021] [Indexed: 05/09/2023]
Abstract
Polished rice is one of the commonly consumed staple foods across the world. However, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising recombinant inbred lines (RILs) for grain Zn and single plant yield, 190 RILs developed from PR116 and Ranbir Basmati were evaluated in two environments (E1 and E2). A subset of 44 contrasting RILs for grain Zn was screened in another two environments (E3 and E4). Phenotypic data was collected for 10 traits, viz., days to 50% flowering, plant height, panicle length, number of tillers, single plant yield (SPY), test weight, Fe and Zn in brown (IBR, ZBR), and polished rice (IPR, ZPR). Stepwise regression analysis of trait data in 190 RILs and a subset of 44 RILs revealed the interdependence of ZPR, ZBR, IPR, and IBR and the negative association of grain Zn with single plant yield. Based on the additive main effect and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) analyses of the subset of 44 RILs across four environments (E1-E4), six promising RILs were identified for ZPR with >28 ppm. Mapping of 190 RILs with 102 simple sequence repeats (SSRs) resulted in 13 QTLs for best linear unbiased estimates (BLUEs) of traits including advantage over check (AOC). Using genotype-based sequencing (GBS), the subset of 44 RILs was mapped with 1035 single-nucleotide polymorphisms (SNPs) and 21 QTLs were identified. More than 100 epistatic interactions were observed. A major QTL qZPR.1.1 (PV 37.84%) and another QTL qZPR.11.1 (PV 15.47%) were identified for grain Zn in polished rice. A common major QTL (qZBR.2.1 and qZPR.2.1) was also identified on chromosome 2 for grain Zn content across SSR and SNP maps. Two potential candidate genes related to transporters were identified based on network analyses in the genomic regions of QTL < 3 Mb. The RILs identified for grain Zn and SPY were nominated for national evaluation as under rice biofortification, and two QTLs identified based on BLUEs could be used in the rice biofortification breeding programs.
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Affiliation(s)
- K. Suman
- ICAR–Indian Institute of Rice Research, Hyderabad, India
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, India
| | - C. N. Neeraja
- ICAR–Indian Institute of Rice Research, Hyderabad, India
- *Correspondence: C. N. Neeraja,
| | - P. Madhubabu
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | | | - Sonali Bej
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | - K. P. Jadhav
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | | | - U. Chaitanya
- ICAR–Indian Institute of Rice Research, Hyderabad, India
| | - Smita C. Pawar
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, India
| | - Surekha H. Rani
- Department of Genetics & Biotechnology, Osmania University, Hyderabad, India
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Gaikwad KB, Rani S, Kumar M, Gupta V, Babu PH, Bainsla NK, Yadav R. Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding. Front Nutr 2020; 7:533453. [PMID: 33324668 PMCID: PMC7725794 DOI: 10.3389/fnut.2020.533453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 09/03/2020] [Indexed: 01/14/2023] Open
Abstract
Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.
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Affiliation(s)
- Kiran B. Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sushma Rani
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Manjeet Kumar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vikas Gupta
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Prashanth H. Babu
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Naresh Kumar Bainsla
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Sahu PK, Mondal S, Sao R, Vishwakarma G, Kumar V, Das BK, Sharma D. Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice ( Oryza sativa L.) landraces. 3 Biotech 2020; 10:487. [PMID: 33123454 DOI: 10.1007/s13205-020-02467-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighbor-joining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.
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Affiliation(s)
- Parmeshwar K Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Vikash Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - B K Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
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Sahoo S, Sanghamitra P, Nanda N, Pawar S, Pandit E, Bastia R, Muduli KC, Pradhan SK. Association of molecular markers with physio-biochemical traits related to seed vigour in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1989-2003. [PMID: 33088044 PMCID: PMC7548267 DOI: 10.1007/s12298-020-00879-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/18/2020] [Accepted: 09/01/2020] [Indexed: 05/08/2023]
Abstract
Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content, superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R2 value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R2 value will be useful for improvement of seed vigour in rice.
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Affiliation(s)
- Swastideepa Sahoo
- Department of Seed Technology, College of Agriculture, OUAT, Bhubaneswar, 751003 Odisha India
| | | | - Nibedita Nanda
- Department of Seed Technology, College of Agriculture, OUAT, Bhubaneswar, 751003 Odisha India
| | - Swapnil Pawar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Ramakrushna Bastia
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
| | - Kumuda Chandra Muduli
- Department of Seed Technology, College of Agriculture, OUAT, Bhubaneswar, 751003 Odisha India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha 753006 India
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28
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Raza Q, Riaz A, Saher H, Bibi A, Raza MA, Ali SS, Sabar M. Grain Fe and Zn contents linked SSR markers based genetic diversity in rice. PLoS One 2020; 15:e0239739. [PMID: 32986755 PMCID: PMC7521695 DOI: 10.1371/journal.pone.0239739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/12/2020] [Indexed: 12/15/2022] Open
Abstract
Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. In this study, we evaluated genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in the representative subset of a large collection of local and exotic rice germplasm. Results demonstrated that aromatic fine grain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions and a strong positive correlation between both mineral elements. Genotyping with 24 trait-linked SSR markers identified 21 polymorphic markers, among which 17 demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating the genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs) contributing 15.41-39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate a wide genetic diversity exist in grain Fe and Zn contents of studied rice accessions and reveal perspective for marker-assisted biofortification breeding.
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Affiliation(s)
- Qasim Raza
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Awais Riaz
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Hira Saher
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Ayesha Bibi
- Plant Pathology Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Mohsin Ali Raza
- Rice Technology Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab Pakistan
| | - Syed Sultan Ali
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
| | - Muhammad Sabar
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Punjab, Pakistan
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Babu PM, Neeraja CN, Rathod S, Suman K, Uttam GA, Chakravartty N, Lachagari VBR, Chaitanya U, Rao LVS, Voleti SR. Stable SNP Allele Associations With High Grain Zinc Content in Polished Rice ( Oryza sativa L.) Identified Based on ddRAD Sequencing. Front Genet 2020; 11:763. [PMID: 32849786 PMCID: PMC7432318 DOI: 10.3389/fgene.2020.00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Polished rice is widely consumed staple food across the globe, however, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising genotypes for grain Zn, a total of 40 genotypes consisting 20 rice landraces, and 20 released high yielding rice varieties were evaluated in three environments (wet seasons 2014, 2015 and 2016) for nine traits including days to 50% flowering (DFF), plant height (PH), panicle length (PL), total number of tillers (TNT), single plant yield (SPY), Fe and Zn in brown (IBR, ZBR) and polished rice (IPR, ZPR). Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) analyses identified genotypes G22 (Edavankudi Pokkali), G17 (Taraori Basmati), G27 (Chittimuthyalu) and G26 (Kalanamak) stable for ZPR and G8 (Savitri) stable for SPY across three environments. Significant negative correlation between yield and grain Zn was reaffirmed. Regression analysis indicated the contribution of traits toward ZPR and SPY and also desirable level of grain Zn in brown rice. A total of 39,137 polymorphic single nucleotide polymorphisms (SNPs) were obtained through double digest restriction site associated DNA (dd-RAD) sequencing of 40 genotypes. Association analyses with nine phenotypic traits revealed 188 stable SNPs with six traits across three environments. ZPR was associated with SNPs located in three putative candidate genes (LOC_Os03g47980, LOC_Os07g47950 and LOC_Os07g48050) on chromosomes 3 and 7. The genomic region of chromosome 7 co localized with reported genomic regions (rMQTL7.1) and OsNAS3 candidate gene. SPY was found to be associated with 12 stable SNPs located in 11 putative candidate genes on chromosome 1, 6, and 12. Characterization of rice landraces and varieties in terms of stability for their grain Zn and yield identified promising donors and recipients along with genomic regions in the present study to be deployed rice Zn biofortification breeding program.
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Affiliation(s)
- P Madhu Babu
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - K Suman
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - G Anurag Uttam
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | | | - U Chaitanya
- ICAR-Indian Institute of Rice Research, Hyderabad, India
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30
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Das P, Adak S, Lahiri Majumder A. Genetic Manipulation for Improved Nutritional Quality in Rice. Front Genet 2020; 11:776. [PMID: 32793287 PMCID: PMC7393646 DOI: 10.3389/fgene.2020.00776] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/30/2020] [Indexed: 01/10/2023] Open
Abstract
Food with higher nutritional value is always desired for human health. Rice is the prime staple food in more than thirty developing countries, providing at least 20% of dietary protein, 3% of dietary fat and other essential nutrients. Several factors influence the nutrient content of rice which includes agricultural practices, post-harvest processing, cultivar type as well as manipulations followed by selection through breeding and genetic means. In addition to mutation breeding, genetic engineering approach also contributed significantly for the generation of nutrition added varieties of rice in the last decade or so. In the present review, we summarize the research update on improving the nutritional characteristics of rice by using genetic engineering and mutation breeding approach. We also compare the conventional breeding techniques of rice with modern molecular breeding techniques toward the generation of nutritionally improved rice variety as compared to other cereals in areas of micronutrients and availability of essential nutrients such as folate and iron. In addition to biofortification, our focus will be on the efforts to generate low phytate in seeds, increase in essential fatty acids or addition of vitamins (as in golden rice) all leading to the achievements in rice nutrition science. The superiority of biotechnology over conventional breeding being already established, it is essential to ascertain that there are no serious negative agronomic consequences for consumers with any difference in grain size or color or texture, when a nutritionally improved variety of rice is generated through genetic engineering technology.
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31
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Barik SR, Pandit E, Mohanty SP, Nayak DK, Pradhan SK. Genetic mapping of physiological traits associated with terminal stage drought tolerance in rice. BMC Genet 2020; 21:76. [PMID: 32664865 PMCID: PMC7362510 DOI: 10.1186/s12863-020-00883-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/02/2020] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Drought during reproductive stage is among the main abiotic stresses responsible for drastic reduction of grain yield in rainfed rice. The genetic mechanism of reproductive stage drought tolerance is very complex. Many physiological and morphological traits are associated with this stress tolerance. Robust molecular markers are required for detection and incorporation of these correlated physiological traits into different superior genetic backgrounds. Identification of gene(s)/QTLs controlling reproductive stage drought tolerance and its deployment in rainfed rice improvement programs are very important. RESULTS QTLs linked to physiological traits under reproductive stage drought tolerance were detected by using 190 F7 recombinant inbred lines (RIL) mapping population of CR 143-2-2 and Krishnahamsa. Wide variations were observed in the estimates of ten physiological traits studied under the drought stress. The RIL population was genotyped using the bulk- segregant analysis (BSA) approach. A total of 77 SSR polymorphic markers were obtained from the parental polymorphisms survey of 401 tested primers. QTL analysis using inclusive composite interval mapping detected a total of three QTLs for the physiological traits namely relative chlorophyll content (qRCC1.1), chlorophyll a (qCHLa1.1), and proline content (qPRO3.1) in the studied RIL population. The QTL, qPRO3.1 is found to be a novel one showing LOD value of 13.93 and phenotypic variance (PVE) of 78.19%. The QTL was located within the marker interval of RM22-RM517 on chromosome 3. Another novel QTL, qRCC1.1 was mapped on chromosome 1 at a distance of 142.8 cM and found to control relative chlorophyll content during terminal drought stress. A third novel QTL was detected in the population that controlled chlorophyll a content (qCHLa1.1) under the terminal stress period. The QTL was located on chromosome 1 at a distance of 81.8 cM and showed 64.5% phenotypic variation. CONCLUSIONS The three novel QTLs, qRCC1.1, qCHLa1.1 and qPRO3.1 controlling relative chlorophyll content, chlorophyll a and proline content, respectively were identified in the mapping population derived from CR 143-2-2 and Krishnahamsa. These 3 QTLs will be useful for enhancement of terminal drought stress tolerance through marker-assisted breeding approach in rice.
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Affiliation(s)
- Saumya Ranjan Barik
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Elssa Pandit
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Shakti Prakash Mohanty
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Deepak Kumar Nayak
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India
| | - Sharat Kumar Pradhan
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753006, India.
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32
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Islam MZ, Arifuzzaman M, Banik S, Hossain MA, Ferdous J, Khalequzzaman M, Pittendrigh BR, Tomita M, Ali MP. Mapping QTLs underpin nutrition components in aromatic rice germplasm. PLoS One 2020; 15:e0234395. [PMID: 32525930 PMCID: PMC7289389 DOI: 10.1371/journal.pone.0234395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.
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Affiliation(s)
- M. Z. Islam
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
| | - M. Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - S. Banik
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. A. Hossain
- Regional Station, Barisal, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - J. Ferdous
- Biotechnology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. Khalequzzaman
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - B. R. Pittendrigh
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - M. Tomita
- Genetics and Genome Engineering Laboratory, Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka City, Shizuoka, Japan
- * E-mail: (MZI); (MPA); (MT)
| | - M. P. Ali
- Entomolgy Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
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Bollinedi H, Yadav AK, Vinod KK, Gopala Krishnan S, Bhowmick PK, Nagarajan M, Neeraja CN, Ellur RK, Singh AK. Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain. Front Genet 2020; 11:213. [PMID: 32391041 PMCID: PMC7188789 DOI: 10.3389/fgene.2020.00213] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/24/2020] [Indexed: 01/16/2023] Open
Abstract
Micronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm accessions, grown at two locations, were evaluated for Fe and Zn in brown rice (BR) and milled rice (MR). A significant variation was observed in the rice germplasm for these micronutrients. The grain Fe concentration was in the range of 6.2–23.1 ppm in BR and 0.8–12.3 ppm in MR, while grain Zn concentration was found to be in the range of 11.0–47.0 ppm and 8.2–40.8 ppm in the BR and MR, respectively. Grain Fe exhibited maximum loss upon milling with a mean retention of 24.9% in MR, while Zn showed a greater mean retention of 74.2% in MR. A genome-wide association study (GWAS) was carried out implementing the FarmCPU model to control the population structure and kinship, and resulted in the identification of 29 marker-trait associations (MTAs) with significant associations for traits viz. FeBR (6 MTAs), FeMR (7 MTAs), ZnBR (11 MTAs), and ZnMR (5 MTAs), which could explain the phenotypic variance from 2.1 to as high as 53.3%. The MTAs governing the correlated traits showed co-localization, signifying the possibility of their simultaneous improvement. The robust MTAs identified in the study could be valuable resource for enhancing Fe and Zn concentration in the rice grain and addressing the problem of Fe and Zn malnutrition among rice consumers.
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Affiliation(s)
- Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashutosh Kumar Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - M Nagarajan
- ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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