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Hurst JP, Yobi A, Li A, Sato S, Clemente TE, Angelovici R, Holding DR. Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment. FRONTIERS IN PLANT SCIENCE 2023; 14:1116886. [PMID: 36998682 PMCID: PMC10043997 DOI: 10.3389/fpls.2023.1116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it's grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus. METHODS A single consensus guide RNA leads to tandem deletion of multiple members of the gene family in addition to the small target site mutations in remaining genes. RNA-seq and ATAC-seq were utilized to identify changes in gene expression and chromatin accessibility in developing kernels in the absence of most alpha-kafirin expression. RESULTS Several differentially accessible chromatin regions and differentially expressed genes were identified. Additionally, several genes upregulated in the edited sorghum line were common with their syntenic orthologues differentially expressed in maize prolamin mutants. ATAC-seq showed enrichment of the binding motif for ZmOPAQUE 11, perhaps indicating the transcription factor's involvement in the kernel response to reduced prolamins. DISCUSSION Overall, this study provides a resource of genes and chromosomal regions which may be involved in sorghum's response to reduced seed storage proteins and the process of proteome rebalancing.
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Affiliation(s)
- J. Preston Hurst
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Abou Yobi
- School of Life Sciences, Ministry of Education, Shandong University, Jinan, China
| | - Aixia Li
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Shirley Sato
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- School of Life Sciences, Ministry of Education, Shandong University, Jinan, China
| | - David R. Holding
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
- Department of Biological Sciences, University of Missouri, Columbia, MO, United States
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Massel K, Hintzsche J, Restall J, Kerr ED, Schulz BL, Godwin ID. CRISPR-knockout of β-kafirin in sorghum does not recapitulate the grain quality of natural mutants. PLANTA 2022; 257:8. [PMID: 36481955 DOI: 10.1007/s00425-022-04038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
When gene editing was applied to knockout beta-kafirin, there was a compensatory increase of gamma-kafirin which does not occur in domesticated null varieties, so enhanced grain quality was not achieved. Sorghum bicolor is an important animal feedstock cereal crop throughout Australia and the southern United States, where its use as a food product is limited by issues with low calorific and nutritive value. Qualities such as reduced digestibility and low essential amino acid content are directly attributed to the kafirin grain storage proteins, the major components of protein bodies within the endosperm. Specifically, the β- and γ-kafirins have few protease cleavage sites and high levels of cysteine residues which lead to a highly cross-linked shell of intra- and inter-molecular disulphide linkages that encapsulate the more digestible α- and δ-kafirins in the core of the protein bodies. Naturally occurring β-kafirin mutants exist and are known to have improved grain quality, with enhanced protein contents and digestibility, traits which are often attributed to the lack of this cysteine-rich kafirin in the mature grain. However, when CRISPR/Cas9 editing was used to create β-kafirin knockout lines, there was no improvement to grain quality in the Tx430 background, although they did have unique protein composition and changes to protein body morphology in the vitreous endosperm. One explanation of the divergence in quality traits found the lines lacking β-kafirin are due to a drastic increase of γ-kafirin which was only found in the gene edited lines. This study highlights that in some germplasm, there is a level of redundancy between the peripheral kafirins, and that improvement of grain protein digestibility cannot be achieved by simply removing the β-kafirin protein in all genetic backgrounds.
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Affiliation(s)
- Karen Massel
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Jessica Hintzsche
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jemma Restall
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian D Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
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Zhao J, Weiss T, Du Z, Hong S, Bean SR, Li Y, Wang D. Comparative evaluation of physicochemical and fermentative responses of three sorghum varieties from dryland and irrigated land and the properties of proteins from distillers’ grains. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Label-free quantitative proteomics of Sorghum bicolor reveals the proteins strengthening plant defense against insect pest Chilo partellus. Proteome Sci 2021; 19:6. [PMID: 33810819 PMCID: PMC8019186 DOI: 10.1186/s12953-021-00173-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spotted stem borer- Chilo partellus - a Lepidopteran insect pest of Sorghum bicolor is responsible for major economic losses. It is an oligophagous pest, which bores through the plant stem, causing 'deadheart' and hampering the development of the main cob. We applied a label-free quantitative proteomics approach on three genotypes of S. bicolor with differential resistance/ susceptibility to insect pests, intending to identify the S. bicolor's systemic protein complement contributing to C. partellus tolerance. METHODS The proteomes of S. bicolor with variable resistance to insect pests, ICSV700, IS2205 (resistant) and Swarna (susceptible) were investigated and compared using label-free quantitative proteomics to identify putative leaf proteins contributing to resistance to C. partellus. RESULTS The multivariate analysis on a total of 967 proteins led to the identification of proteins correlating with insect resistance/susceptibility of S. bicolor. Upon C. partellus infestation S. bicolor responded by suppression of protein and amino acid biosynthesis, and induction of proteins involved in maintaining photosynthesis and responding to stresses. The gene ontology analysis revealed that C. partellus-responsive proteins in resistant S. bicolor genotypes were mainly involved in stress and defense, small molecule biosynthesis, amino acid metabolism, catalytic and translation regulation activities. At steady-state, the resistant S. bicolor genotypes displayed at least two-fold higher numbers of unique proteins than the susceptible genotype Swarna, mostly involved in catalytic activities. Gene expression analysis of selected candidates was performed on S. bicolor by artificial induction to mimic C. partellus infestation. CONCLUSION The collection of identified proteins differentially expressed in resistant S. bicolor, are interesting candidates for further elucidation of their role in defense against insect pests.
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Selle PH, Hughes RJ, Godwin ID, Khoddami A, Chrystal PV, Liu SY. Addressing the shortfalls of sorghum as a feed grain for chicken-meat production. WORLD POULTRY SCI J 2021. [DOI: 10.1080/00439339.2020.1866966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Peter H. Selle
- Poultry Research Foundation within the University of Sydney, Camden, Australia
| | - Robert J Hughes
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia
| | - Ian D. Godwin
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia Qld, Australia
| | - Ali Khoddami
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Peter V. Chrystal
- Poultry Research Foundation within the University of Sydney, Camden, Australia
- Baiada Poultry Pty Limited, Pendle Hill, Australia
| | - Sonia Yun Liu
- Poultry Research Foundation within the University of Sydney, Camden, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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Kimani W, Zhang LM, Wu XY, Hao HQ, Jing HC. Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor). BMC Genomics 2020; 21:112. [PMID: 32005168 PMCID: PMC6995107 DOI: 10.1186/s12864-020-6538-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study. RESULTS Levels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study. CONCLUSION Promising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.
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Affiliation(s)
- Wilson Kimani
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Huai-Qing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Liu G, Gilding EK, Kerr ED, Schulz BL, Tabet B, Hamaker BR, Godwin ID. Increasing protein content and digestibility in sorghum grain with a synthetic biology approach. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Weerasooriya DK, Bean SR, Nugusu Y, Ioerger BP, Tesso TT. The effect of genotype and traditional food processing methods on in-vitro protein digestibility and micronutrient profile of sorghum cooked products. PLoS One 2018; 13:e0203005. [PMID: 30192773 PMCID: PMC6128525 DOI: 10.1371/journal.pone.0203005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/13/2018] [Indexed: 11/19/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is one of the principal staple for millions of people in sub-Saharan Africa serving as the main sources of protein. However, protein digestibility is low in sorghum and this may be affected by processing methods. In this study 15 sorghum cultivars and one variety each of maize (Zea maize) and tef (Eragrostis tef) all of Ethiopian origin were investigated for in-vitro protein digestibility (IVPD), activity and concentration of anti-nutritional factors and micro nutrient profile in raw flour and various cooked food samples. Kafirin composition content and composition was also determined from raw flour samples of the sorghum cultivars. IVPD was significantly different between genotypes with both maize and tef superior to sorghum both in cooked and uncooked state except for the high lysine genotype Wetet Be-gunchie. Cooking significantly reduced IVPD in all crops but had only minor effect in maize. Results revealed a highly significant interaction between genotype and food processing methods where, occasionally, genotypes with highest IVPD under one processing method ended up to be the lowest under another. Trypsin inhibitor levels had a significant and negative correlation with IVPD (r2 = 0.1), while changes in phytic acid concentration and intrinsic phytase levels during processing followed opposite trends to each other. Processing increased mineral levels by 20-44% for iron and 4-29% for zinc perhaps due to degradation of phytic acid. Results demonstrated that protein digestibility and the concentration of anti- nutritional factors varied widely depending on the food type. Identification of specific genotypes for a specific food product may help improve the nutritional quality of sorghum based foods.
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Affiliation(s)
| | - Scott R. Bean
- United States Department of Agriculture-Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Yohannes Nugusu
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Brian P. Ioerger
- United States Department of Agriculture-Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Tesfaye T. Tesso
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
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Emendack Y, Burke J, Bean S, Wilson J, Hayes C, Laza H. Composition, functional components, and physical characteristics of grain from staygreen and senescent sorghum lines grown under variable water availability. Cereal Chem 2018. [DOI: 10.1002/cche.10077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yves Emendack
- Plant Stress and Germplasm Development Research; USDA-ARS; Lubbock Texas
| | - John Burke
- Plant Stress and Germplasm Development Research; USDA-ARS; Lubbock Texas
| | - Scott Bean
- Grain Quality and Structure Research; USDA-ARS; Manhattan Kansas
| | - Jeff Wilson
- Grain Quality and Structure Research; USDA-ARS; Manhattan Kansas
| | - Chad Hayes
- Plant Stress and Germplasm Development Research; USDA-ARS; Lubbock Texas
| | - Haydee Laza
- Plant and Soil Science Department; Texas Tech University; Lubbock Texas
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Taylor J, Taylor JRN. Making Kafirin, the Sorghum Prolamin, into a Viable Alternative Protein Source. J AM OIL CHEM SOC 2018. [DOI: 10.1002/aocs.12016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Janet Taylor
- Institute for Food, Nutrition and Well-being and Department of Food Science; University of Pretoria, Private Bag X20; Hatfield 0028 South Africa
| | - John R. N. Taylor
- Institute for Food, Nutrition and Well-being and Department of Food Science; University of Pretoria, Private Bag X20; Hatfield 0028 South Africa
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Selle PH, Moss AF, Truong HH, Khoddami A, Cadogan DJ, Godwin ID, Liu SY. Outlook: Sorghum as a feed grain for Australian chicken-meat production. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2018; 4:17-30. [PMID: 30167480 PMCID: PMC6112367 DOI: 10.1016/j.aninu.2017.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/24/2022]
Abstract
This review is an outlook for sorghum as a feed grain for broiler chickens based on a survey of relevant stake-holders and recent research outcomes. Australian grain sorghum production will probably continue to generate a harvest in the order of 2.5 × 106 t of which some 7.9 × 105 t will be used as a feed grain for poultry and pigs. Feed grains are included primarily to provide energy from starch, but energy utilisation by broiler chickens offered sorghum-based diets is relatively inferior, because of incomplete starch digestion. Kafirin, the dominant protein fraction, 'non-tannin' phenolic compounds and phytate are 3 'starch extrinsic' factors in sorghum that compromise starch digestibility and energy utilisation in broiler chickens offered sorghum-based diets. Kafirin concentrations in 6 sorghum varieties were negatively correlated with metabolizable energy to gross energy (ME:GE) ratios (r = -0.891; P < 0.02) or the efficiency of energy utilisation in broiler chickens. Importantly, kafirin proportions of sorghum protein may be increasing with time in Australia. If so, this represents a fundamental challenge to sorghum breeders which presumably could be met by the development of sorghum varieties with different characteristics, especially in relation to the γ- and β-kafirin fractions. White sorghum varieties contain lower polyphenol concentrations which should be advantageous as concentrations of total phenolic compounds were negatively correlated to ME:GE ratios (r = -0.838; P < 0.04) in 6 sorghum varieties. It would be desirable if more white varieties were to become available. It is suggested that responses to exogenous phytase in birds offered sorghum-based diets would be more robust if sorghum were to contain lower concentrations of kafirin and phenolic compounds. Paradoxically, while better sorghum varieties almost certainly could be developed, it may not necessarily follow that they will command a price premium from poultry and pig producers.
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Affiliation(s)
- Peter H. Selle
- Poultry Research Foundation, The University of Sydney, Camden, NSW 2570, Australia
| | - Amy F. Moss
- Poultry Research Foundation, The University of Sydney, Camden, NSW 2570, Australia
| | - Ha H. Truong
- Poultry Research Foundation, The University of Sydney, Camden, NSW 2570, Australia
| | - Ali Khoddami
- Poultry Research Foundation, The University of Sydney, Camden, NSW 2570, Australia
- Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, NSW 2006, Australia
| | | | - Ian D. Godwin
- School of Agriculture and Food Sciences, The University of Queensland, QLD 4072, Australia
| | - Sonia Y. Liu
- Poultry Research Foundation, The University of Sydney, Camden, NSW 2570, Australia
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Cremer JE, Bean SR, Tilley MM, Ioerger BP, Ohm JB, Kaufman RC, Wilson JD, Innes DJ, Gilding EK, Godwin ID. Grain sorghum proteomics: integrated approach toward characterization of endosperm storage proteins in kafirin allelic variants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9819-9831. [PMID: 25177767 DOI: 10.1021/jf5022847] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Grain protein composition determines quality traits, such as value for food, feedstock, and biomaterials uses. The major storage proteins in sorghum are the prolamins, known as kafirins. Located primarily on the periphery of the protein bodies surrounding starch, cysteine-rich β- and γ-kafirins may limit enzymatic access to internally positioned α-kafirins and starch. An integrated approach was used to characterize sorghum with allelic variation at the kafirin loci to determine the effects of this genetic diversity on protein expression. Reversed-phase high performance liquid chromatography and lab-on-a-chip analysis showed reductions in alcohol-soluble protein in β-kafirin null lines. Gel-based separation and liquid chromatography-tandem mass spectrometry identified a range of redox active proteins affecting storage protein biochemistry. Thioredoxin, involved in the processing of proteins at germination, has reported impacts on grain digestibility and was differentially expressed across genotypes. Thus, redox states of endosperm proteins, of which kafirins are a subset, could affect quality traits in addition to the expression of proteins.
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Affiliation(s)
- Julia E Cremer
- School of Agriculture and Food Sciences and ⊥Institute for Molecular Bioscience, The University of Queensland , St Lucia, Brisbane, QLD 4072, Australia
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