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Zhao W, Zhang R, Zhou L, Zhang Z, Du F, Wu R, Kong J, An S. Construction and optimization of a genetic transformation system for efficient expression of human insulin-GFP fusion gene in flax. BIORESOUR BIOPROCESS 2024; 11:83. [PMID: 39190215 DOI: 10.1186/s40643-024-00799-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024] Open
Abstract
The human insulin gene modified with a C-peptide was synthesized according to the plant-preferred codon, and a fusion gene expression vector of insulin combined with green fluorescent protein (GFP) was constructed. The optimization of the flax callus culturing was undertaken, and a more efficient Agrobacterium-mediated genetic transformation of the flax hypocotyls was achieved. The critical concentration values of hygromycin on the flax hypocotyl development, as well as on its differentiated callus, were explored by the method of antibiotic gradient addition, and the application of antibiotic screening for the verification of positive calluses was assessed. The fusion gene of insulin and GFP was successfully inserted into the flax genome and expressed, as confirmed through polymerase chain reaction and Western blotting. In conclusion, we have established a flax callus culture system suitable for insulin expression. By optimizing the conditions of the flax callus induction, transformation, screening, and verification of a transgenic callus, we have provided an effective way to obtain insulin. Moreover, the herein-employed flax callus culture system could provide a feasible, cheap, and environmentally friendly platform for producing bioactive proteins.
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Affiliation(s)
- Wei Zhao
- School of Medicine, Hebei University of Engineering, Handan Economic and Technological Development Zone, No. 19 Taiji Road, Handan, Hebei Province, 056038, China
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China
| | - Rui Zhang
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China
- The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Changan District, Shijiazhuang, Hebei, 050000, China
| | - Luyang Zhou
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China
- Shijiazhuang Medical College, No.1 Tongxin Road, Lingshou County, Shijiazhuang, Hebei, 050500, China
| | - Zhongxia Zhang
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China
| | - Fei Du
- Department of Ultrasound Medicine, Hengshui People's Hospital, Hengshui, Hebei, 053000, China
| | - Ruoyu Wu
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China.
| | - Jing Kong
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China.
| | - Shengjun An
- Hebei Provincial Engineering Laboratory of Plant Bioreactor Preparation Technology, Hebei University of Chinese Medicine, No. 326 Xinshi South Road, Qiaoxi District, Shijiazhuang, Hebei, 050090, China.
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Guo D, Jiang H, Xie L. An R2R3-MYB Transcriptional Factor LuMYB314 Associated with the Loss of Petal Pigmentation in Flax ( Linum usitatissimum L.). Genes (Basel) 2024; 15:511. [PMID: 38674445 PMCID: PMC11050253 DOI: 10.3390/genes15040511] [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: 03/22/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The loss of anthocyanin pigments is one of the most common evolutionary transitions in petal color, yet the genetic basis for these changes in flax remains largely unknown. In this study, we used crossing studies, a bulk segregant analysis, genome-wide association studies, a phylogenetic analysis, and transgenic testing to identify genes responsible for the transition from blue to white petals in flax. This study found no correspondence between the petal color and seed color, refuting the conclusion that a locus controlling the seed coat color is associated with the petal color, as reported in previous studies. The locus controlling the petal color was mapped using a BSA-seq analysis based on the F2 population. However, no significantly associated genomic regions were detected. Our genome-wide association study identified a highly significant QTL (BP4.1) on chromosome 4 associated with flax petal color in the natural population. The combination of a local Manhattan plot and an LD heat map identified LuMYB314, an R2R3-MYB transcription factor, as a potential gene responsible for the natural variations in petal color in flax. The overexpression of LuMYB314 in both Arabidopsis thaliana and Nicotiana tabacum resulted in anthocyanin deposition, indicating that LuMYB314 is a credible candidate gene for controlling the petal color in flax. Additionally, our study highlights the limitations of the BSA-seq method in low-linkage genomic regions, while also demonstrating the powerful detection capabilities of GWAS based on high-density genomic variation mapping. This study enhances our genetic insight into petal color variations and has potential breeding value for engineering LuMYB314 to develop colored petals, bast fibers, and seeds for multifunctional use in flax.
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Affiliation(s)
- Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
| | - Haixia Jiang
- Key Laboratory of Plant Stress Biology in Arid Land, College of Life Science, Xinjiang Normal University, Urumqi 830017, China;
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China;
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Abtahi M, Mirlohi A. Quality assessment of flax advanced breeding lines varying in seed coat color and their potential use in the food and industrial applications. BMC PLANT BIOLOGY 2024; 24:60. [PMID: 38254037 PMCID: PMC10804595 DOI: 10.1186/s12870-024-04733-1] [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: 10/23/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND With the increasing consumer awareness of the strong relationship between food and health, flax became a promising functional food due to its bioactive nutraceutical composition. Intra-specific crosses of eight contrasting flax genotypes were performed previously, and within segregating F6 progeny families, we investigated a close-up composition of phytochemicals derived from whole seeds. RESULTS The considerable genetic variation among the flax F6 families suggested that intra-specific hybridization is essential in flax breeding to obtain and broaden genetic variability and largely affirmed the opportunity for selecting promising lines. Also, significant variations in the targeted metabolite contents and antioxidant properties were observed among brown and yellow-seeded families. Notably, brown-seeded families expressed the highest average values of saturated fatty acids, protein, fiber, tocopherol, phenolics, SDG, and SECO lignans. Yellow-seeded families represented the highest average content of unsaturated fatty acids and mucilage. The cultivation year significantly affects flaxseed's composition and functional properties, presumably due to temperature, humidity, and sunshine time differences. Interestingly, the seeds obtained in warmer conditions were more potent and had more chemical constituents. The favorable genetic correlations among all evaluated traits suggest the possibility of joint genetic selection for several nutritional and phytochemical characteristics in flax. The current study highlights the importance and utilization of 19 top families as their seeds and oil play imperative roles in the pharmaceuticals and food industries. The antioxidant capacity of the seeds showed that families 84B, 23B, 35Y, 95Y, 30B, 88B, and 78B serve as a natural source of dietary antioxidants beneficial to human health. To increase the oxidative stability of the flaxseed oil, the quality evaluation identified some families with low levels of linolenic acid. CONCLUSIONS These findings are essential to improving flaxseed's nutritional quality and therapeutic properties through a bulk breeding program.
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Affiliation(s)
- Mozhgan Abtahi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Isfahan, 84156-83111, Iran.
| | - Aghafakhr Mirlohi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Isfahan, 84156-83111, Iran
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Abtahi M, Mirlohi A, Sharif-Moghaddam N, Ataii E. Revealing seed color variation and their possible association with yield and quality traits in a diversity panel of flax ( Linum Usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1038079. [PMID: 36438141 PMCID: PMC9691844 DOI: 10.3389/fpls.2022.1038079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Seed color is a vital quality determinant of flax, significant for consumers' acceptability, and determines the commercial values of seeds. Also, seed color as a phenotypic marker may be a convenient way to select the plants with desired traits. This study assessed a diversity panel representing 144 flax genotypes from diverse geographical origins for the existence of genetic variability for luminosity (L*) and chromaticity (a* and b*) seed color parameters, seed yield, and quality traits over two years. The genetic variance was significant for seed color parameters, demonstrating the presence of significant genetic variability, which provides a resource to objectively evaluate and select flax genotypes based on seed color according to the market demand. High heritability combined with the high genotypic coefficient of variation observed for seed yield, oil, and protein content suggested a better genetic gain upon selecting these traits. Seed yield, seed quality traits, and phenological traits showed significant negative correlation with L* and b* parameters and positive correlation with a* suggesting that the seeds' dark background and brown color can serve as marker characters to prescreen early-flowering, high-yielding and oil and protein-rich genotypes. Interestingly 48 brown-seeded genotypes were identified as early-flowering with short height, large seeds, high thousand seed weight, and capsule diameter. In addition, 34 genotypes were characterized by light-colored yellow seeds, large seeds, late-flowering with shorter height, and high branch numbers. Our results highlighted that North America and Australia-belonged genotypes were lighter yellow-seeded than the ones from other continents. Flax genotypes from South America and Asia were high-yielding, while genotypes from North America were low-yielding genotypes. Moreover, darker brown-seeded genotypes have prevailed in the South American continent.
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Affiliation(s)
- Mozhgan Abtahi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Li J, Xin W, Wang W, Zhao S, Xu L, Jiang X, Duan Y, Zheng H, Yang L, Liu H, Jia Y, Zou D, Wang J. Mapping of Candidate Genes in Response to Low Nitrogen in Rice Seedlings. RICE (NEW YORK, N.Y.) 2022; 15:51. [PMID: 36243857 PMCID: PMC9569405 DOI: 10.1186/s12284-022-00597-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen is not only a macronutrient essential for crop growth and development, but also one of the most critical nutrients in farmland ecosystem. Insufficient nitrogen supply will lead to crop yield reduction, while excessive application of nitrogen fertilizer will cause agricultural and eco-environment damage. Therefore, mining low-nitrogen tolerant rice genes and improving nitrogen use efficiency are of great significance to the sustainable development of agriculture. This study was conducted by Genome-wide association study on a basis of two root morphological traits (root length and root diameter) and 788,396 SNPs of a natural population of 295 rice varieties. The transcriptome of low-nitrogen tolerant variety (Longjing 31) and low-nitrogen sensitive variety (Songjing 10) were sequenced between low and high nitrogen treatments. A total of 35 QTLs containing 493 genes were mapped. 3085 differential expressed genes were identified. Among these 493 genes, 174 genes showed different haplotype patterns. There were significant phenotype differences among different haplotypes of 58 genes with haplotype differences. These 58 genes were hypothesized as candidate genes for low nitrogen tolerance related to root morphology. Finally, six genes (Os07g0471300, Os11g0230400, Os11g0229300, Os11g0229400, Os11g0618300 and Os11g0229333) which expressed differentially in Longjing 31 were defined as more valuable candidate genes for low-nitrogen tolerance. The results revealed the response characteristics of rice to low-nitrogen, and provided insights into regulatory mechanisms of rice to nitrogen deficiency.
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Affiliation(s)
- Jia Li
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Wei Xin
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Weiping Wang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Shijiao Zhao
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Lu Xu
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Xingdong Jiang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Yuxuan Duan
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Hongliang Zheng
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Luomiao Yang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Hualong Liu
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Yan Jia
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China
| | - Detang Zou
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China.
| | - Jingguo Wang
- College of Agriculture, Northeast Agricultural University/Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education, Harbin, 150030, Heilongjiang Province, People's Republic of China.
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Abtahi M, Mirlohi A, Zare S. Selection of promising lines for yield and quality traits in advanced segregating generation of linseed. J AM OIL CHEM SOC 2022. [DOI: 10.1002/aocs.12632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mozhgan Abtahi
- Department of Agronomy and Plant Breeding, College of Agriculture Isfahan University of Technology Isfahan Iran
| | - Aghafakhr Mirlohi
- Department of Agronomy and Plant Breeding, College of Agriculture Isfahan University of Technology Isfahan Iran
| | - Sara Zare
- Department of Agronomy and Plant Breeding, College of Agriculture Isfahan University of Technology Isfahan Iran
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Yu Y, Yang Z, Jiang Y, Wang L, Wu Y, Liao J, Yang R, Zhang L. Inheritance and QTL Mapping for Flower Color in Salvia miltiorrhiza Bunge. J Hered 2022; 113:248-256. [PMID: 35259262 DOI: 10.1093/jhered/esac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022] Open
Abstract
Salvia miltiorrhiza Bunge is an outcross-pollinated plant with diverse flower colors, ranging from white to purple. To clarify the genetic basis of S. miltiorrhiza flower color, we crossed white-flowered S. miltiorrhiza f. alba with dark violet-flowered S. miltiorrhiza, and selfed F1 to obtain an F2 population. The RGB color system was used to describe the flower color of the parents, F1 progeny, and F2 individuals. Afterward, we used genotyping-by-sequencing (GBS) technology to construct a high-density linkage map of S. miltiorrhiza based on the F2 population. Finally, the linkage map was used to locate the QTLs of the genes that control flower color in S. miltiorrhiza. Through measurement and cluster analysis of the R, G, and B values of flowers from the parents, F1, and F2 individuals, it was found that the purple flower color of S. miltiorrhiza is a quantitative trait controlled by two loci of major genes. The genetic map contained 605 SNPs with a total length of 738.3 cM in eight linkage groups (LGs), and the average distance between two markers was 1.22 cM. Based on the constructed genetic map and the flower R, G, B, and R+G+B values, two QTLs were detected for flower color, located on LG4 and LG5. The results of this study lay the foundation for cloning genes that control flower color and studying the molecular mechanism of flower color regulation in S. miltiorrhiza.
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Affiliation(s)
- Yan Yu
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zaijun Yang
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Yuanyuan Jiang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Long Wang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Yichao Wu
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Jinqiu Liao
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Ruiwu Yang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Li Zhang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
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Young L, Akhov L, Kulkarni M, You F, Booker H. Fine-mapping of a putative glutathione S-transferase (GST) gene responsible for yellow seed colour in flax (Linum usitatissimum). BMC Res Notes 2022; 15:72. [PMID: 35184755 PMCID: PMC8859895 DOI: 10.1186/s13104-022-05964-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Objective The brown seed coat colour of flax (Linum ustiatissimum) results from proanthocyanidin synthesis and accumulation. Glutathione S-transferases (GSTs), such as the TT19 protein in Arabidopsis, have been implicated in the transport of anthocyanidins during the synthesis of the brown proanthocyanidins. This study fine mapped the g allele responsible for yellow seed colour in S95407 and identified it as a putative mutated GST. Results We developed a Recombinant Inbred Line population with 320 lines descended from a cross between CDC Bethune (brown seed coat) and S95407 (yellow seed) and used molecular markers to fine map the G gene on Chromosome 6 (Chr 6). We used Next Generation Sequencing (NGS) to identify a putative GST was identified in this region and Sanger sequenced the gene from CDC Bethune, S95407 and other yellow seeded genotypes. The putative GST from S95407 had 13 SNPs encoding, including four non-synonymous amino acid changes, compared to the CDC Bethune reference sequence and the other genotypes. The GST encoded by Lus10019895 is a lambda-GST in contrast to the Arabidopsis TT19 which is a phi-GST. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-05964-x.
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Affiliation(s)
- Lester Young
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7H 3R2, Canada.
| | - Leonid Akhov
- National Research Council Saskatoon, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Manoj Kulkarni
- National Research Council Saskatoon, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Frank You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Crop Science Building, 50 Stone Road E, Guelph, ON, N1G 2W1, Canada
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Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
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Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
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Soto-Cerda BJ, Cloutier S, Quian R, Gajardo HA, Olivos M, You FM. Genome-Wide Association Analysis of Mucilage and Hull Content in Flax ( Linum usitatissimum L.) Seeds. Int J Mol Sci 2018; 19:ijms19102870. [PMID: 30248911 PMCID: PMC6213135 DOI: 10.3390/ijms19102870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million single nucleotide polymorphism (SNP) markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome-wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 kb. Seven and four quantitative trait loci (QTL) were identified for MC and HC, respectively. Promising candidate genes identified include Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17, and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE. These genes have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal MC and HC composition for food and feed by genomic-based breeding.
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Affiliation(s)
- Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Rocío Quian
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Humberto A Gajardo
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Marcos Olivos
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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Zhang J, Long Y, Wang L, Dang Z, Zhang T, Song X, Dang Z, Pei X. Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.). BMC PLANT BIOLOGY 2018. [PMID: 30086718 DOI: 10.1186/s128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND Flax is an important field crop that can be used for either oilseed or fiber production. Plant height and technical length are important characters for flax. For linseed flax, plants usually have a short technical length and plant height than those for fiber flax. As an important agronomical character for fiber and linseed flax, plant height is usually a selection target for breeding. However, because of limited technologies and methods available, there has been little research focused on discovering the molecular mechanism controlling plant height. RESULTS In this study, two related recombinant inbred line (RIL) populations developed from crosses of linseed and fiber parents were developed and phenotyped for plant height and technical length in four environments. A consensus linkage map based on two RIL populations was constructed using SNP markers generated by genotyping by sequencing (GBS) technology. A total of 4497 single nucleotide polymorphism (SNP) markers were included on 15 linkage groups with an average marker density of one marker every 2.71 cM. Quantitative trait locus (QTL) mapping analysis was performed for plant height and technical length using the two populations. A total of 19 QTLs were identified for plant height and technical length. For the MH population, eight plant height QTLs and seven technical length QTLs were identified, five of which were common QTLs for both traits. For the PH population, six plant height and three technical length QTLs were identified. By comparing the QTLs and candidate gene information in the two population, two common QTLs and three candidate genes were discovered. CONCLUSIONS This study provides a foundation for map-based cloning of QTLs and marker-assisted selection for plant height-related traits in linseed and fiber flax.
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Affiliation(s)
- Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liming Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Zhao Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Tianbao Zhang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaxia Song
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanhai Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China.
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zhang J, Long Y, Wang L, Dang Z, Zhang T, Song X, Dang Z, Pei X. Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.). BMC PLANT BIOLOGY 2018; 18:160. [PMID: 30086718 PMCID: PMC6081803 DOI: 10.1186/s12870-018-1366-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/16/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Flax is an important field crop that can be used for either oilseed or fiber production. Plant height and technical length are important characters for flax. For linseed flax, plants usually have a short technical length and plant height than those for fiber flax. As an important agronomical character for fiber and linseed flax, plant height is usually a selection target for breeding. However, because of limited technologies and methods available, there has been little research focused on discovering the molecular mechanism controlling plant height. RESULTS In this study, two related recombinant inbred line (RIL) populations developed from crosses of linseed and fiber parents were developed and phenotyped for plant height and technical length in four environments. A consensus linkage map based on two RIL populations was constructed using SNP markers generated by genotyping by sequencing (GBS) technology. A total of 4497 single nucleotide polymorphism (SNP) markers were included on 15 linkage groups with an average marker density of one marker every 2.71 cM. Quantitative trait locus (QTL) mapping analysis was performed for plant height and technical length using the two populations. A total of 19 QTLs were identified for plant height and technical length. For the MH population, eight plant height QTLs and seven technical length QTLs were identified, five of which were common QTLs for both traits. For the PH population, six plant height and three technical length QTLs were identified. By comparing the QTLs and candidate gene information in the two population, two common QTLs and three candidate genes were discovered. CONCLUSIONS This study provides a foundation for map-based cloning of QTLs and marker-assisted selection for plant height-related traits in linseed and fiber flax.
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Affiliation(s)
- Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Yan Long
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Liming Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Zhao Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Tianbao Zhang
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaxia Song
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhanhai Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070 China
| | - Xinwu Pei
- Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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