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Alafari HA, Freeg H, Abdelrahman M, Attia KA, Jalal AS, El-Banna A, Aboshosha A, Fiaz S. Integrated analysis of yield response and early stage biochemical, molecular, and gene expression profiles of pre-breeding rice lines under water deficit stress. Sci Rep 2024; 14:17855. [PMID: 39090142 PMCID: PMC11294455 DOI: 10.1038/s41598-024-60863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/29/2024] [Indexed: 08/04/2024] Open
Abstract
Breeding high yielding water-deficit tolerant rice is considered a primary goal for achieving the objectives of the sustainable development goals, 2030. However, evaluating the performance of the pre-breeding-promising parental-lines for water deficit tolerance prior to their incorporation in the breeding program is crucial for the success of the breeding programs. The aim of the current investigation is to assess the performance of a set of pre-breeding lines compared with their parents. To achieve this goal a set of 7 pre-breeding rice lines along with their parents (5 genotypes) were field evaluated under well-irrigated and water-stress conditions. Water stress was applied by flush irrigation every 12 days without keeping standing water after irrigation. Based on the field evaluation results, a pre-breeding line was selected to conduct physiological and expression analysis of drought related genes at the green house. Furthermore, a greenhouse trial was conducted in pots, where the genotypes were grown under well and stress irrigation conditions at seedling stage for physiological analysis and expression profiling of the genotypes. Results indicated that the pre-breeding lines which were high yielding under water shortage stress showed low drought susceptibility index. Those lines exhibited high proline, SOD, TSS content along with low levels of MDA content in their leaves. Moreover, the genotypes grain yield positively correlated with proline, SOD, TSS content in their leaves. The SSR markers RM22, RM525, RM324 and RM3805 were able to discriminate the tolerant parents from the sensitive one. Expression levels of the tested drought responsive genes revealed the upregulation of OsLEA3, OsAPX2, OsNAC1, OSDREB2A, OsDREB1C, OsZIP23, OsP5CS, OsAHL1 and OsCATA genes in response to water deficit stress as compared to their expression under normal irrigated condition. Taken together among the tested pre-breeding lines the RBL112 pre-breeding line is high yielding under water-deficit and could be used as donor for high yielding genes in the breeding for water deficit resistance. This investigation withdraws attention to evaluate the promising pre-breeding lines before their incorporation in the water deficit stress breeding program.
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Affiliation(s)
- Hayat Ali Alafari
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - Haytham Freeg
- Rice Biotechnology Lab., Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Mohamed Abdelrahman
- Rice Biotechnology Lab., Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt.
| | - Kotb A Attia
- Rice Biotechnology Lab., Rice Research and Training Center, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
- Center of Excellence in Biotechnology Research, King Saud University, P.O. Box 2455-11451, 11451, Riyadh, Saudi Arabia
| | - Areej S Jalal
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia.
| | - Antar El-Banna
- Center of Excellence in Biotechnology Research, King Saud University, P.O. Box 2455-11451, 11451, Riyadh, Saudi Arabia
| | - Ali Aboshosha
- Center of Excellence in Biotechnology Research, King Saud University, P.O. Box 2455-11451, 11451, Riyadh, Saudi Arabia
| | - Sajid Fiaz
- Department of Genetics, College of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
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Geng S, Gao W, Li S, Chen Q, Jiao Y, Zhao J, Wang Y, Wang T, Qu Y, Chen Q. Rapidly mining candidate cotton drought resistance genes based on key indicators of drought resistance. BMC PLANT BIOLOGY 2024; 24:129. [PMID: 38383284 PMCID: PMC10880307 DOI: 10.1186/s12870-024-04801-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Focusing on key indicators of drought resistance is highly important for quickly mining candidate genes related to drought resistance in cotton. RESULTS In the present study, drought resistance was identified in drought resistance-related RIL populations during the flowering and boll stages, and multiple traits were evaluated; these traits included three key indicators: plant height (PH), single boll weight (SBW) and transpiration rate (Tr). Based on these three key indicators, three groups of extreme mixing pools were constructed for BSA-seq. Based on the mapping interval of each trait, a total of 6.27 Mb QTL intervals were selected on chromosomes A13 (3.2 Mb), A10 (2.45 Mb) and A07 (0.62 Mb) as the focus of this study. Based on the annotation information and qRT‒PCR analysis, three key genes that may be involved in the drought stress response of cotton were screened: GhF6'H1, Gh3AT1 and GhPER55. qRT‒PCR analysis of parental and extreme germplasm materials revealed that the expression of these genes changed significantly under drought stress. Cotton VIGS experiments verified the important impact of key genes on cotton drought resistance. CONCLUSIONS This study focused on the key indicators of drought resistance, laying the foundation for the rapid mining of drought-resistant candidate genes in cotton and providing genetic resources for directed molecular breeding of drought resistance in cotton.
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Affiliation(s)
- Shiwei Geng
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Wenju Gao
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Shengmei Li
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Qin Chen
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yang Jiao
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Jieyin Zhao
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yuxiang Wang
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - TingWei Wang
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Yanying Qu
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China
| | - Quanjia Chen
- 1Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, 830052, China.
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Dwiningsih Y, Thomas J, Kumar A, Gupta C, Gill N, Ruiz C, Alkahtani J, Baisakh N, Pereira A. QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population. Int J Mol Sci 2023; 24:15167. [PMID: 37894848 PMCID: PMC10606886 DOI: 10.3390/ijms242015167] [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: 07/31/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.
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Affiliation(s)
- Yheni Dwiningsih
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA;
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Charles Ruiz
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Jawaher Alkahtani
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Niranjan Baisakh
- Department of School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
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Ghazy MI, Hamad HS, Gewaily EE, Bleih EM, Arafat EFA, El-Kallawy WH, El-Naem SA, Rehan M, Alwutayd KM, Abd El Moneim D. Impacts of kinetin implementation on leaves, floral and root-related traits during seed production in hybrid rice under water deficiency. BMC PLANT BIOLOGY 2023; 23:398. [PMID: 37605164 PMCID: PMC10463769 DOI: 10.1186/s12870-023-04405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Water deficit is one of the most significant abiotic factors affecting rice and agricultural production worldwide. In hybrid rice, cytoplasmic male sterility (CMS) is an important technique for creating high-yielding crop based on heterosis. The phytohormone kinetin (Kin) regulates cell division in plant during the early stages of grain formation, as well as flow assimilation and osmotic regulation under water stress. The present study performed to estimate the effects of irrigation intervals (irrigation each six days (I6), nine days (I9), twelve days (I12) and fifteen days (I15) against continuous flooding (CF, each three days)) and kinetin exogenously application (control, 15 mg L-1 and 30 mg L-1) on hybrid rice (L1, IR69625A; L2, G46A and R, Giza 178 R) seed production. RESULTS Leaves traits (Chlorophyll content (CHC), relative water content (RWC), stomatal conductance (SC), Leaf temperature (LT) and transpiration rate (TR)), floral traits such as style length (SL) and total stigma length (TSL), in addition to root traits (i.e., root length (RL), root volume (RV), root: shoot ratio (RSR), root thickness (RT), root xylem vessels number (RXVN) and root xylem vessel area (RXVA) were evaluated and a significant enhancement in most traits was observed. Applying 30 mg L-1 kinetin significantly and positively enhanced all growth, floral and roots traits (RV and RXVA recorded the most increased values by 14.8% and 23.9%, respectively) under prolonging irrigation intervals, in comparison to non-treated plants. CONCLUSIONS Subsequently, spraying kinetin exogenously on foliar could be an alternative method to reduce the harmful influences of water deficiency during seed production in hybrid rice.
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Affiliation(s)
- Mohamed I Ghazy
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Hassan Sh Hamad
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Elsayed E Gewaily
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Eman M Bleih
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Elsayed F A Arafat
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Wael H El-Kallawy
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Sabry A El-Naem
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Kafrelsheikh, 33717, Egypt
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, 51452, Buraydah, Saudi Arabia
- Department of Genetics, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia
| | - Diaa Abd El Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511, Egypt.
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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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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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Molecular mapping of drought-responsive QTLs during the reproductive stage of rice using a GBS (genotyping-by-sequencing) based SNP linkage map. Mol Biol Rep 2023; 50:65-76. [PMID: 36306008 DOI: 10.1007/s11033-022-08002-y] [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: 08/08/2022] [Accepted: 10/03/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND In rice, drought stress at reproductive stage drastically reduces yield, which in turn hampers farmer's efforts towards crop production. The majority of the rice varieties have resistance genes against several abiotic and biotic stresses. Therefore, the traditional landraces were studied to identify QTLs/candidate genes associated with drought tolerance. METHODS AND RESULTS A high-density SNP-based genetic map was constructed using a Genotyping-by-sequencing (GBS) approach. The recombinant inbred lines (RILs) derived from crossing 'Banglami × Ranjit' were used for QTL analysis. A total map length of 1306.424 cM was constructed, which had an average inter-marker distance of 0.281 cM. The phenotypic evaluation of F6 and F7 RILs were performed under drought stress and control conditions. A total of 42 QTLs were identified under drought stress and control conditions for yield component traits explaining 1.95-13.36% of the total phenotypic variance (PVE). Among these, 19 QTLs were identified under drought stress conditions, whereas 23 QTLs were located under control conditions. A total of 4 QTLs explained a PVE ≥ 10% which are considered as the major QTLs. Moreover, bioinformatics analysis revealed the presence of 6 candidate genes, which showed differential expression under drought and control conditions. CONCLUSION These QTLs/genes may be deployed for marker-assisted pyramiding to improve drought tolerance in the existing rice varieties.
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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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9
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Raj SRG, Nadarajah K. QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals. Int J Mol Sci 2022; 24:ijms24010006. [PMID: 36613450 PMCID: PMC9820233 DOI: 10.3390/ijms24010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.
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Zia MAB, Yousaf MF, Asim A, Naeem M. An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice). Mol Biol Rep 2022; 49:12077-12090. [DOI: 10.1007/s11033-022-08036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
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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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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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