1
|
Fagan RJ, Eskildsen D, Catanzano T, Stanietzky R, Kamel S, Eltaher M, Elsayes KM. Burnout and the role of mentorship for radiology trainees and early career radiologists. Diagn Interv Radiol 2024; 30:313-317. [PMID: 38836503 DOI: 10.4274/dir.2024.242825] [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] [Indexed: 06/06/2024]
Abstract
Burnout is a widespread issue among physicians, including radiologists and radiology trainees. Long hours, isolation, and substantial stress levels contribute to healthcare workers experiencing a substantially higher rate of burnout compared with other professionals. Resident physicians, continuously exposed to stressors such as new clinical situations and performance feedback, are particularly susceptible. Mentorship has proven to be an effective strategy in mitigating burnout. Various mentorship delivery models exist, all aiming to have mentors serve as role models to mentees, thereby alleviating stress and anxiety. Physician groups and healthcare enterprises have actively implemented these programs, recognizing them as both successful and cost-effective. This article explores different mentorship models, their implementation processes, and the effectiveness of these programs as a standard component of academic departments.
Collapse
Affiliation(s)
- Richard J Fagan
- Baylor College of Medicine, Department of Radiology, Texas, United States of America
| | - Dane Eskildsen
- Baylor College of Medicine, Department of Radiology, Texas, United States of America
| | - Tara Catanzano
- University of Massachusetts Medical School-Baystate, Department of Radiology, UMass Chan-Baystate, Springfield, United States of America
| | - Rachel Stanietzky
- University of Texas MD Anderson Cancer Center, Department of Abdominal Imaging, Texas, United States of America
| | - Serageldin Kamel
- University of Texas MD Anderson Cancer Center, Department of Abdominal Imaging, Texas, United States of America
| | - Mohamed Eltaher
- University of Texas MD Anderson Cancer Center, Department of Abdominal Imaging, Texas, United States of America
| | - Khaled M Elsayes
- University of Texas MD Anderson Cancer Center, Department of Abdominal Imaging, Texas, United States of America
| |
Collapse
|
2
|
Alam M, Wang Y, Chen J, Lou G, Yang H, Zhou Y, Luitel S, Jiang G, He Y. QTL detection for rice grain storage protein content and genetic effect verifications. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:89. [PMID: 38059164 PMCID: PMC10695898 DOI: 10.1007/s11032-023-01436-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01436-7.
Collapse
Affiliation(s)
- Mufid Alam
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - YingYing Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Jianxian Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Guangming Lou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Yin Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Saurav Luitel
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Gonghao Jiang
- College of Life Science, Heilongjiang University, Haerbin, 150080 Heilongjiang China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| |
Collapse
|
3
|
Generating waxy rice starch with target type of amylopectin fine structure and gelatinization temperature by waxy gene editing. Carbohydr Polym 2023; 306:120595. [PMID: 36746586 DOI: 10.1016/j.carbpol.2023.120595] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/31/2022] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Waxy rice, which lacks amylose, is an important variant in rice, and its starches have been widely used. New waxy rice varieties generated via the CRISPR/Cas9 gene-editing system is described. Herein, four waxy rice starches with different physicochemical properties were successfully obtained by the CRISPR/Cas9 editing Waxy (Wx) gene. The results showed that the amylose content (AC) of wx mutant starches ranged from 0.26 to 1.78 %, and CZBwx1 starches had the best gel consistency and highest water solubility among all wx mutants. Mutations of Wxb allele produced more short-chains (degree of chain polymerization (DP) 6-11), and less medium- and long-chains (DP12-70) than that of Wxa, while the AC of Wxa allele mutants was higher than the mutations of Wxb allele. The gelatinization temperature (GT) of wxa mutant starches was higher than that of wxb mutant starches. Moreover, we found that the GT and amylopectin fine structure type of waxy rice starch did not change after Wx gene editing. Based on these findings, it is possible to produce waxy rice starch with different physicochemical properties, containing target GT and chain length distributions of amylopectin.
Collapse
|
4
|
Fu Y, Luo T, Hua Y, Yan X, Liu X, Liu Y, Liu Y, Zhang B, Liu R, Zhu Z, Zhu J. Assessment of the Characteristics of Waxy Rice Mutants Generated by CRISPR/Cas9. FRONTIERS IN PLANT SCIENCE 2022; 13:881964. [PMID: 35755680 PMCID: PMC9226628 DOI: 10.3389/fpls.2022.881964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
The cooking and eating quality of rice grains is a major focus from a consumer's perspective and is mainly determined by the apparent amylose content (AAC) of the starch. Waxy rice, a type of rice with an AAC of less than 2%, is an important goal for the breeding of high-quality rice. In recent years, the cloning of the Waxy (Wx) gene has revealed the molecular mechanism of the formation of waxy traits in rice. However, there have been limited studies on the physicochemical properties, such as gelatinization temperature, rapid viscosity analyzer profile, and amylopectin fine structure of wx mutants. In the current study, a rapid and highly efficient strategy was developed through the CRISPR/Cas9 gene-editing system for generating wx mutants in the background of five different rice varieties. The wx mutation significantly reduced the AAC and starch viscosity but did not affect the major agronomic traits (such as plant height, panicle number per plant, grain number per panicle, and seed-setting frequency). Incorporation of the wx mutation into varieties with low initial AAC levels resulted in further reduction in AAC, but without significantly affecting the original, desirable gelatinization traits and amylopectin structure types, suggesting that parents with low initial AAC should be preferred in breeding programs.
Collapse
Affiliation(s)
- Yuhao Fu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tingting Luo
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Yonghuan Hua
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Xuehai Yan
- Leshan Municipal Bureau of Agriculture and Rural Affairs, Leshan, China
| | - Xu Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Ying Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Baoli Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Rui Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Zizhong Zhu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
| | - Jun Zhu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
5
|
Applications of Starch Biopolymers for a Sustainable Modern Agriculture. SUSTAINABILITY 2022. [DOI: 10.3390/su14106085] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protected cultivation in modern agriculture relies extensively on plastic-originated mulch films, nets, packaging, piping, silage, and various applications. Polyolefins synthesized from petrochemical routes are vastly consumed in plasticulture, wherein PP and PE are the dominant commodity plastics. Imposing substantial impacts on our geosphere and humankind, plastics in soil threaten food security, health, and the environment. Mismanaged plastics are not biodegradable under natural conditions and generate problematic emerging pollutants such as nano-micro plastics. Post-consumed petrochemical plastics from agriculture face many challenges in recycling and reusing due to soil contamination in fulfilling the zero waste hierarchy. Hence, biodegradable polymers from renewable sources for agricultural applications are pragmatic as mitigation. Starch is one of the most abundant biodegradable biopolymers from renewable sources; it also contains tunable thermoplastic properties suitable for diverse applications in agriculture. Functional performances of starch such as physicomechanical, barrier, and surface chemistry may be altered for extended agricultural applications. Furthermore, starch can be a multidimensional additive for plasticulture that can function as a filler, a metaphase component in blends/composites, a plasticizer, an efficient carrier for active delivery of biocides, etc. A substantial fraction of food and agricultural wastes and surpluses of starch sources are underutilized, without harnessing useful resources for agriscience. Hence, this review proposes reliable solutions from starch toward timely implementation of sustainable practices, circular economy, waste remediation, and green chemistry for plasticulture in agriscience
Collapse
|
6
|
Ni D, Yang F, Lin L, Sun C, Ye X, Wang L, Kong X. Interrelating Grain Hardness Index of Wheat with Physicochemical and Structural Properties of Starch Extracted Therefrom. Foods 2022; 11:foods11081087. [PMID: 35454674 PMCID: PMC9025240 DOI: 10.3390/foods11081087] [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: 03/25/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/05/2023] Open
Abstract
To investigate the physicochemical, structural, and rheological characteristics of starch from wheat cultivars varying in grain hardness index employed in making jiuqu and to interrelate grain hardness index with physicochemical and structural properties of starch. Starch extracted therefrom was investigated for structural and physicochemical properties. Starch granules showed relatively wide granule size distribution; large size granules showed lenticular shapes while medium and small size granules exhibited spherical or irregular shapes. Starch from wheat with a lower grain hardness index exhibited a relatively higher degree of crystallinity. Chain-length profiles of amylopectin showed distinct differences; among the fractions of fa, fb1, fb2, and fb3 representing the weight-based chain-length proportions in amylopectin, the fa fractions ranged from 19.7% to 21.6%, the fb1 fractions ranged from 44.4% to 45.6%, the fb2 fractions ranged from 16.2% to 17.0%, and the fb3 fractions ranged from 16.1% to 18.8%, respectively. To, Tp, Tc, and ∆H of starch ranged from 57.8 to 59.7 °C, 61.9 to 64.2 °C, 67.4 to 69.8 °C, and 11.9 to 12.7 J/g, respectively. Peak viscosity, hot pasting viscosity, cool pasting viscosity, breakdown, and setback of starch ranged from 127 to 221 RVU, 77 to 106 RVU, 217 to 324 RVU, 44 to 116 RVU, and 137 to 218 RVU, respectively. Both G’ and G” increased in the frequency range of 0.628 to 125.6 rad/s; the wheat starch gels were more solid-like during the whole range of frequency sweep.
Collapse
Affiliation(s)
- Derang Ni
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (D.N.); (X.Y.)
- Kweichow Moutai Corporation Limited, Renhuai 564501, China; (F.Y.); (L.L.)
| | - Fan Yang
- Kweichow Moutai Corporation Limited, Renhuai 564501, China; (F.Y.); (L.L.)
| | - Lin Lin
- Kweichow Moutai Corporation Limited, Renhuai 564501, China; (F.Y.); (L.L.)
| | - Chongde Sun
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Xingqian Ye
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; (D.N.); (X.Y.)
| | - Li Wang
- Kweichow Moutai Group, Renhuai 564501, China
- Correspondence: (L.W.); (X.K.)
| | - Xiangli Kong
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
- Correspondence: (L.W.); (X.K.)
| |
Collapse
|
7
|
Showkat QA, Majid D, Rather JA, Naqash S, Dar BN, Makroo HA. Drying of lotus rhizome slices: Influence of drying conditions on Fourier transform infrared spectroscopy, rheology, functional, and physicochemical characteristics of lotus rhizome powder. J FOOD PROCESS ENG 2022. [DOI: 10.1111/jfpe.13954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qazi A. Showkat
- Department of Food Technology Islamic University of Science and Technology Awantipora India
| | - Darakshan Majid
- Department of Food Technology Islamic University of Science and Technology Awantipora India
| | - Jahangir A. Rather
- Department of Food Technology Islamic University of Science and Technology Awantipora India
| | - Saadiya Naqash
- Division of Food Science and Technology SKUAST‐K Srinagar India
| | - Basharat N. Dar
- Department of Food Technology Islamic University of Science and Technology Awantipora India
| | - Hilal A. Makroo
- Department of Food Technology Islamic University of Science and Technology Awantipora India
| |
Collapse
|
8
|
Genetic mapping for grain quality and yield-attributed traits in Basmati rice using SSR-based genetic map. J Biosci 2021. [DOI: 10.1007/s12038-021-00169-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
9
|
Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A. Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 2021; 11:10082. [PMID: 33980871 PMCID: PMC8115083 DOI: 10.1038/s41598-021-87964-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/19/2021] [Indexed: 02/03/2023] Open
Abstract
Increasing trends in the occurrence of diabetes underline the need to develop low glycemic index (GI) rice with preferred grain quality. In the current study, a diverse set of 3 K sub-panel of rice consisting of 150 accessions was evaluated for resistant starch and predicted glycemic index, including nine other quality traits under transplanted situation. Significant variations were noticed among the accessions for the traits evaluated. Trait associations had shown that amylose content possess significant positive and negative association with resistant starch and predicted glycemic index. Genome-wide association studies with 500 K SNPs based on MLM model resulted in a total of 41 marker-trait associations (MTAs), which were further confirmed and validated with mrMLM multi-locus model. We have also determined the allelic effect of identified MTAs for 11 targeted traits and found favorable SNPs for 8 traits. A total of 11 genes were selected for haplo-pheno analysis to identify the superior haplotypes for the target traits where haplotypes ranges from 2 (Os10g0469000-GC) to 15 (Os06g18720-AC). Superior haplotypes for RS and PGI, the candidate gene Os06g11100 (H4-3.28% for high RS) and Os08g12590 (H13-62.52 as intermediate PGI). The identified superior donors possessing superior haplotype combinations may be utilized in Haplotype-based breeding to developing next-generation tailor-made high quality healthier rice varieties suiting consumer preference and market demand.
Collapse
Affiliation(s)
- Ramchander Selvaraj
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Arun Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Vikas Kumar Singh
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Sonali Vijay Habde
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Uma Maheshwar Singh
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India
| | - Arvind Kumar
- IRRI South Asia Hub (IRRI-SAH), ICRISAT Campus, Patancheru, Hyderabad, India.
- South-Asia Regional Centre (SARC), International Rice Research Institute (IRRI), Varanasi, India.
| |
Collapse
|
10
|
Physicochemical and structural properties of sago starch. Int J Biol Macromol 2020; 164:1785-1793. [DOI: 10.1016/j.ijbiomac.2020.07.310] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/17/2020] [Accepted: 07/29/2020] [Indexed: 01/30/2023]
|
11
|
Liu Y, Chen X, Xu Y, Xu Z, Li H, Sui Z, Corke H. Gel texture and rheological properties of normal amylose and waxy potato starch blends with rice starches differing in amylose content. Int J Food Sci Technol 2020. [DOI: 10.1111/ijfs.14826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi Liu
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai200240China
| | - Xiaojing Chen
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai200240China
| | - Yijuan Xu
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai200240China
| | - Zekun Xu
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai200240China
| | - Haitao Li
- School of Food Science and Technology Jiangnan University Wuxi214122China
| | - Zhongquan Sui
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai200240China
| | - Harold Corke
- Biotechnology and Food Engineering Program Guangdong Technion‐Israel Institute of Technology Shantou515063China
- Faculty of Biotechnology and Food Engineering Technion–Israel Institute of Technology Haifa3200003Israel
| |
Collapse
|
12
|
Wang H, Zhu Q, Wu T, Zhang M. Glass transition temperature, rheological, and gelatinization properties of high amylose corn starch and waxy cassava starch blends. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Han Wang
- State Key Laboratory of Food Nutrition and Safety Tianjin University of Science & Technology Tianjin China
- Engineering Research Center of Food Biotechnology Ministry of Education Tianjin University of Science & Technology Tianjin China
| | - Qiaomei Zhu
- State Key Laboratory of Food Nutrition and Safety Tianjin University of Science & Technology Tianjin China
- Engineering Research Center of Food Biotechnology Ministry of Education Tianjin University of Science & Technology Tianjin China
| | - Tao Wu
- State Key Laboratory of Food Nutrition and Safety Tianjin University of Science & Technology Tianjin China
- Engineering Research Center of Food Biotechnology Ministry of Education Tianjin University of Science & Technology Tianjin China
| | - Min Zhang
- State Key Laboratory of Food Nutrition and Safety Tianjin University of Science & Technology Tianjin China
- Engineering Research Center of Food Biotechnology Ministry of Education Tianjin University of Science & Technology Tianjin China
| |
Collapse
|
13
|
Lee SI, Park JW, Kwon SJ, Jo YD, Hong MJ, Kim JB, Choi HI. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. PLANTS 2020; 9:plants9091088. [PMID: 32847097 PMCID: PMC7570246 DOI: 10.3390/plants9091088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.
Collapse
|
14
|
Qu P, Shi J, Chen T, Chen K, Shen C, Wang J, Zhao X, Ye G, Xu J, Zhang L. Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice. RICE (NEW YORK, N.Y.) 2020; 13:13. [PMID: 32060661 PMCID: PMC7021868 DOI: 10.1186/s12284-020-0373-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/04/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice. RESULTS We constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis. CONCLUSIONS In this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.
Collapse
Affiliation(s)
| | | | - Tianxiao Chen
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518210, China
| | - Kai Chen
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518210, China
| | - Congcong Shen
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518210, China
| | - Jiankang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiangqian Zhao
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China
| | - Guoyou Ye
- Genetics and Biotechnology Division, International Rice Research Institute, Baños, Laguna, Philippines
| | - Jianlong Xu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Luyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
15
|
Ma M, Wen Y, Qiu C, Zhan Q, Sui Z, Corke H. Milling affects rheological and gel textural properties of rice flour. Cereal Chem 2019. [DOI: 10.1002/cche.10236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mengting Ma
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Yadi Wen
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Chen Qiu
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Qian Zhan
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Zhongquan Sui
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| | - Harold Corke
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai China
| |
Collapse
|
16
|
Viana VE, Pegoraro C, Busanello C, Costa de Oliveira A. Mutagenesis in Rice: The Basis for Breeding a New Super Plant. FRONTIERS IN PLANT SCIENCE 2019; 10:1326. [PMID: 31781133 PMCID: PMC6857675 DOI: 10.3389/fpls.2019.01326] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
The high selection pressure applied in rice breeding since its domestication thousands of years ago has caused a narrowing in its genetic variability. Obtaining new rice cultivars therefore becomes a major challenge for breeders and developing strategies to increase the genetic variability has demanded the attention of several research groups. Understanding mutations and their applications have paved the way for advances in the elucidation of a genetic, physiological, and biochemical basis of rice traits. Creating variability through mutations has therefore grown to be among the most important tools to improve rice. The small genome size of rice has enabled a faster release of higher quality sequence drafts as compared to other crops. The move from structural to functional genomics is possible due to an array of mutant databases, highlighting mutagenesis as an important player in this progress. Furthermore, due to the synteny among the Poaceae, other grasses can also benefit from these findings. Successful gene modifications have been obtained by random and targeted mutations. Furthermore, following mutation induction pathways, techniques have been applied to identify mutations and the molecular control of DNA damage repair mechanisms in the rice genome. This review highlights findings in generating rice genome resources showing strategies applied for variability increasing, detection and genetic mechanisms of DNA damage repair.
Collapse
Affiliation(s)
| | | | | | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Faculdade de Agronomia Eliseu Maciel, Departamento de Fitotecnia, Universidade Federal de Pelotas, Campus Capão do Leão, Rio Grande do Sul, Brazil
| |
Collapse
|
17
|
Ma M, He M, Xu Y, Li P, Li Z, Sui Z, Corke H. Thermal processing of rice grains affects the physical properties of their pregelatinised rice flours. Int J Food Sci Technol 2019. [DOI: 10.1111/ijfs.14417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mengting Ma
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China
| | - Meng He
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China
| | - Yijuan Xu
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China
| | - Peng Li
- Department of Food Science and Engineering Qingdao Agricultural University Qingdao 266109 China
| | - Zijun Li
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhongquan Sui
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China
| | - Harold Corke
- Department of Food Science & Technology School of Agriculture and Biology Shanghai Jiao Tong University Shanghai 200240 China
| |
Collapse
|
18
|
Tangsrianugul N, Wongsagonsup R, Suphantharika M. Physicochemical and rheological properties of flour and starch from Thai pigmented rice cultivars. Int J Biol Macromol 2019; 137:666-675. [DOI: 10.1016/j.ijbiomac.2019.06.196] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/14/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022]
|
19
|
Lin L, Pan T, Liu Q, Wei C. Cooking, morphological, mechanical and digestion properties of cooked rice with suppression of starch branching enzymes. Int J Biol Macromol 2019; 137:187-196. [PMID: 31255622 DOI: 10.1016/j.ijbiomac.2019.06.210] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
Kernel components and some physicochemical properties of cooked rice were investigated and compared between a popular japonica rice Wu-xiang 9915 (WX) and its transgenic line (WX-SBEI/IIb-) with suppression of starch branching enzyme I/IIb. The starch content, especially amylopectin content, was significantly lower in WX-SBEI/IIb- than in WX. Brown rice flour had markedly higher gelatinization temperature in WX-SBEI/IIb- than in WX. The cooked kernels of WX-SBEI/IIb- had significantly lower volume swelling, leached material amount and wet weight than those of WX during cooking. Starch granules in WX kernel could be gelatinized completely and gradually from the exterior to the interior of endosperm, leading to breakage of cooked kernels. However, aggregate, elongated and small starch granules in the exterior of WX-SBEI/IIb- endosperm could not be gelatinized completely and remained their morphologies during cooking, leading to a high resistance of kernels to cooking. Brown rice flour of WX-SBEI/IIb- had significantly lower pasting viscosities, storage modulus and loss modulus but higher loss angle tangent than that of WX. The cooked kernels of WX-SBEI/IIb- had considerably higher hardness, springiness and cohesiveness but lower adhesiveness than those of WX. The starch in cooked kernels was more resistant to digestion in WX-SBEI/IIb- than in WX.
Collapse
Affiliation(s)
- Lingshang Lin
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Ting Pan
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Qiaoquan Liu
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
| | - Cunxu Wei
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
| |
Collapse
|
20
|
Bazrkar-Khatibani L, Fakheri BA, Hosseini-Chaleshtori M, Mahender A, Mahdinejad N, Ali J. Genetic Mapping and Validation of Quantitative Trait Loci (QTL) for the Grain Appearance and Quality Traits in Rice ( Oryza sativa L.) by Using Recombinant Inbred Line (RIL) Population. Int J Genomics 2019; 2019:3160275. [PMID: 30931320 PMCID: PMC6410440 DOI: 10.1155/2019/3160275] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 01/22/2023] Open
Abstract
Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. In order to understand the genetic components of grain appearance traits in paddy, brown, and head rice, 15 traits were evaluated by using 157 recombinant inbred lines (RILs) derived from a cross between two Iranian rice cultivars Ali-Kazemi (A) and Kadous (K). A significant variation was observed and showed transgressive segregation among the RILs. Correlations between the visual appearances of grain traits were studied. A linkage map with 65 polymorphic SSR markers was constructed, which covered 1517.32 cM of the rice genome. A total of seven QTLs were identified on four chromosomes, 1, 6, 9, and 12, associated with four traits, which are explained by the total phenotypic variation of 44.27% and LOD score of 32.77 in 2014 and 2015, respectively. Among these, four QTLs for two traits were consistently flanked by RM23904 and RM24432 on chromosome 9. Single QTL for head grain length (HGL) expressed in both the years on chromosomes 1 and 9. A major QTL for seed weight was detected on chromosome 9, which explained 10.18% of the phenotypic variation. The additive effect of all the QTLs was positively contributed by Ali-Kazemi allele, except one QTL on chromosome 6 (qBGL_6) that showed a negative additive effect being contributed by the Kadous allele. The study also validated the identified QTLs with the polymorphic SSR markers that were previously reported. Novel QTLs were identified on chromosomes 6 and 9, and many of the polymorphic markers were found to be associated with milling processing of grain quality, cooking, and nutraceutical properties of rice by extensive literature and database analysis. Therefore, these validated QTLs and marker information could be utilized in the marker-assisted selection to improve grain appearance and nutritional grain quality traits in rice.
Collapse
Affiliation(s)
| | | | - Maryam Hosseini-Chaleshtori
- Rice Research Institute of Iran (RRII), Agricultural Research, Education and Extension Organization, Rasht 1658, Iran
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines
| | | | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines
| |
Collapse
|
21
|
Ito VC, Schnitzler E, Demiate IM, Eusébio MES, Lacerda LG, Castro RAE. Physicochemical, Thermal, Crystallographic, and Morphological Properties of Biodynamic Black Rice Starch, and of Residual Fractions From Aqueous Extraction. STARCH-STARKE 2018. [DOI: 10.1002/star.201700348] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vivian C. Ito
- Food Science and Technology Graduate Program, State University of Ponta Grossa (UEPG); Av. Carlos Cavalcanti 4748 Uvaranas Campus CEP 84.030-900 Ponta Grossa, PR Brazil
| | - Egon Schnitzler
- Food Science and Technology Graduate Program, State University of Ponta Grossa (UEPG); Av. Carlos Cavalcanti 4748 Uvaranas Campus CEP 84.030-900 Ponta Grossa, PR Brazil
| | - Ivo Mottin Demiate
- Food Science and Technology Graduate Program, State University of Ponta Grossa (UEPG); Av. Carlos Cavalcanti 4748 Uvaranas Campus CEP 84.030-900 Ponta Grossa, PR Brazil
| | | | - Luiz Gustavo Lacerda
- Food Science and Technology Graduate Program, State University of Ponta Grossa (UEPG); Av. Carlos Cavalcanti 4748 Uvaranas Campus CEP 84.030-900 Ponta Grossa, PR Brazil
| | - Ricardo A. E. Castro
- CQC, Chemistry Department University of Coimbra; R. Larga, CEP 3004-535 Coimbra Portugal
- Faculty of Pharmacy, University of Coimbra; R. Azinhaga de Santa Comba CEP 3000-548, Coimbra Portugal
| |
Collapse
|
22
|
|
23
|
|
24
|
Chen L, Gao W, Chen S, Wang L, Zou J, Liu Y, Wang H, Chen Z, Guo T. High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. RICE (NEW YORK, N.Y.) 2016; 9:48. [PMID: 27659284 PMCID: PMC5033801 DOI: 10.1186/s12284-016-0121-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/14/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study. RESULTS A RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization. CONCLUSION QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.
Collapse
Affiliation(s)
- Likai Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Weiwei Gao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Siping Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Liping Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Jiyong Zou
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Agricultural Technology Extension, Guangzhou, 510520, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
25
|
|