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Qiu CW, Ma Y, Gao ZF, Sreesaeng J, Zhang S, Liu W, Ahmed IM, Cai S, Wang Y, Zhang G, Wu F. Genome-wide profiling of genetic variations reveals the molecular basis of aluminum stress adaptation in Tibetan wild barley. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132541. [PMID: 37716271 DOI: 10.1016/j.jhazmat.2023.132541] [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: 07/06/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Aluminum (Al) toxicity in acidic soil is a major factor affecting crop productivity. The extensive genetic diversity found in Tibetan wild barley germplasms offers a valuable reservoir of alleles associated with aluminum tolerance. Here, resequencing of two Al-tolerant barley genotypes (Tibetan wild barley accession XZ16 and cultivated barley Dayton) identified a total of 19,826,182 and 16,287,277 single nucleotide polymorphisms (SNPs), 1628,052 and 1386,973 insertions/deletions (InDels), 61,532 and 57,937 structural variations (SVs), 248,768 and 240,723 copy number variations (CNVs) in XZ16 and Dayton, respectively, and uncovered approximately 600 genes highly related to Al tolerance in barley. Comparative genomic analyses unveiled 71 key genes that contain unique genetic variants in XZ16 and are predominantly associated with organic acid exudation, Al sequestration, auxin response, and transcriptional regulation. Manipulation of these key genes at the genetic and transcriptional level is a promising strategy for developing optimal haplotype combinations and new barley cultivars with improved Al tolerance. This study represents the first comprehensive examination of genetic variation in Al-tolerant Tibetan wild barley through genome-wide profiling. The obtained results make the deep insight into the mechanisms underlying barley adaptation to Al toxicity, and identified the candidate genes useful for improvement of Al tolerance in barley.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Zi-Feng Gao
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Jakkrit Sreesaeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Shuo Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Wenxing Liu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Imrul Mosaddek Ahmed
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Plant Biotechnology Laboratory, Center for Viticulture & Small Fruit Research, Florida A&M University, FL 32317, USA
| | - Shengguan Cai
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.
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Jing Y, Bian L, Zhang X, Zhao B, Zheng R, Su S, Ye D, Zheng X, El-Kassaby YA, Shi J. Genetic diversity and structure of the 4 th cycle breeding population of Chinese fir ( Cunninghamia lanceolata (lamb.) hook). FRONTIERS IN PLANT SCIENCE 2023; 14:1106615. [PMID: 36778690 PMCID: PMC9911867 DOI: 10.3389/fpls.2023.1106615] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi ) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.
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Affiliation(s)
- Yonglian Jing
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Bian
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xuefeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Benwen Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Shunde Su
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Daiquan Ye
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Xueyan Zheng
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Zhang Y, Shi J, Shen C, To VT, Shi Q, Ye L, Shi J, Zhang D, Chen W. Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars. PLANT CELL REPORTS 2022; 41:2279-2292. [PMID: 36209436 DOI: 10.1007/s00299-022-02920-8] [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: 06/19/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars. Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deletions) have become popular because of their abundance and ease of detection, discovery of genome-wide DNA polymorphisms and development of InDel markers in barley have lagged behind other cereal crops such as rice, maize and wheat. In this study, we re-sequenced two barley cultivars, Golden Promise (GP, a classic British spring barley variety) and Hua30 (a Chinese spring barley variety), and mapped clean reads to the reference Morex genome, and identified in total 13,933,145 single nucleotide polymorphisms (SNPs) and 1,240,456 InDels for GP with Morex, 11,297,100 SNPs and 781,687 InDels for Hua30 with Morex, and 13,742,399 SNPs and 1,191,597 InDels for GP with Hua30. We further characterized distinct types, chromosomal distribution patterns, genome location, functional effect, and other features of these DNA polymorphisms. Additionally, we revealed the functional relevance of these identified SNPs/InDels regarding different flowering times between Hua30 and GP within 17 flowering time genes. Furthermore, we developed a series of InDel markers and validated them experimentally in 43 barley core accessions, respectively. Finally, we rebuilt population structure and phylogenetic tree of these 43 barley core accessions. Collectively, all of these genetic resources will facilitate not only the basic research but also applied research in barley.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Vinh-Trieu To
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingzhen Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia, 5064, Australia.
| | - Weiwei Chen
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia, 5064, Australia.
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Chen Z, He Y, Iqbal Y, Shi Y, Huang H, Yi Z. Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq. BMC Genomics 2022; 23:43. [PMID: 35012465 PMCID: PMC8751252 DOI: 10.1186/s12864-021-08277-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 12/22/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. RESULTS We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. CONCLUSIONS As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.
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Affiliation(s)
- Zhiyong Chen
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Yancen He
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yasir Iqbal
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yanlan Shi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hongmei Huang
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Zili Yi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
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Wang W, Zhang L. Genome-Wide Association Study on Two Immune-Related Traits in Jinghai Yellow Chicken. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2021-1587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- W Wang
- Jiangsu Agri-animal Husbandry Vocational College, China; Yangzhou University, China
| | - L Zhang
- Jiangsu Agri-animal Husbandry Vocational College, China
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Zakeel MCM, Alam M, Geering ADW, Topp B, Akinsanmi OA. Discovery of Single Nucleotide Polymorphisms for Resistance to Abnormal Vertical Growth in Macadamia. FRONTIERS IN PLANT SCIENCE 2021; 12:756815. [PMID: 35003155 PMCID: PMC8739493 DOI: 10.3389/fpls.2021.756815] [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: 08/11/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked sample analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance.
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Affiliation(s)
- Mohamed Cassim Mohamed Zakeel
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Mobashwer Alam
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Nambour, QLD, Australia
| | - Andrew D. W. Geering
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Bruce Topp
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Nambour, QLD, Australia
| | - Olufemi A. Akinsanmi
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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Luo H, Hill CB, Zhou G, Zhang XQ, Li C. Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley. BMC PLANT BIOLOGY 2020; 20:346. [PMID: 32698771 PMCID: PMC7374919 DOI: 10.1186/s12870-020-02547-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/08/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Drought is projected to become more frequent and severe in a changing climate, which requires deep sowing of crop seeds to reach soil moisture. Coleoptile length is a key agronomic trait in cereal crops such as barley, as long coleoptiles are linked to drought tolerance and improved seedling establishment under early water-limited growing conditions. RESULTS In this study, we detected large genetic variation in a panel of 328 diverse barley (Hordeum vulgare L.) accessions. To understand the overall genetic basis of barley coleoptile length, all accessions were germinated in the dark and phenotyped for coleoptile length after 2 weeks. The investigated barleys had significant variation for coleoptile length. We then conducted genome-wide association studies (GWASs) with more than 30,000 molecular markers and identified 8 genes and 12 intergenic loci significantly associated with coleoptile length in our barley panel. The Squamosa promoter-binding-like protein 3 gene (SPL3) on chromosome 6H was identified as a major candidate gene. The missense variant on the second exon changed serine to alanine in the conserved SBP domain, which likely impacted its DNA-binding activity. CONCLUSION This study provides genetic loci for seedling coleoptile length along with candidate genes for future potential incorporation in breeding programmes to enhance early vigour and yield potential in water-limited environments.
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Affiliation(s)
- Hao Luo
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Gaofeng Zhou
- Department of Primary Industries and Regional Development, Agriculture and Food, South Perth, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia.
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Wang W, He J, Chen S, Peng P, Zhong W, Wang X, Zhang T, Li Y. Construction of a high-density genetic map and fine mapping of a candidate gene locus for a novel branched-spike mutant in barley. PLoS One 2020; 15:e0227617. [PMID: 31914168 PMCID: PMC6948822 DOI: 10.1371/journal.pone.0227617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/24/2019] [Indexed: 11/19/2022] Open
Abstract
A Yunnan branched-spike (Ynbs) barley mutant is useful for study of the genetic mechanisms underlying variation in barley spike architecture. In the current study, a mutant (Ynbs-1), a recombinant inbred line (RIL-1), and a cultivar (BDM-8) were used as parents to develop populations. Ynbs-1 exhibits typical branched spike, whereas the others exhibit six-row spike. Genetic analysis on their F1, F2 and F3 populations showed that one recessive gene is responsible for the branched spike trait. SLAF marker generated from specific locus amplified fragment sequencing (SLAF-seq) was used to genotype the populations. A high-density genetic map of barley was constructed using 14,348 SLAF markers, which covered all 7 chromosomes at 1,347.44 cM in length with an average marker density of 0.09 cM between adjacent markers. Linkage analysis of the branched-spike trait using the genetic map indicated that branched spike trait in the Ynbs-1 is controlled by single locus on chromosome 2H at the interval between 65.00 and 65.47 cM that is flanked by Marker310119 and Marker2679451. Several candidate genes that may be responsible for barley multiple-spikelet degeneration, single-floret spikelet increase and seed set rate decrease were identified in the region. The high-density genetic map and the gene locus revealed in this study provide valuable information for elucidating the genetic mechanism of spike branching in barley.
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Affiliation(s)
- Weibin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junyu He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shengwei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- * E-mail:
| | - Peng Peng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei Zhong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xintian Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Tingting Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuping Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
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Watt C, Zhou G, McFawn LA, Chalmers KJ, Li C. Fine mapping of qGL5H, a major grain length locus in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:883-893. [PMID: 30465063 DOI: 10.1007/s00122-018-3243-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 11/16/2018] [Indexed: 05/05/2023]
Abstract
A major grain length QTL on chromosome 5H was fine mapped from 180.5 to 1.7 Mb. Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing barley yield and grain physical quality. Using data from four independent environments and molecular marker genotype data, we identified 23 significant QTLs for these four traits, ten of which were consensus QTLs and identified in two or more environments. A QTL region on chromosome 5H designated qGL5H that was associated with grain size was fine mapped to a 1.7 Mb interval. qGL5H was able to explain 21.6% of phenotypic variation for grain length within the population. This major QTL is an appropriate candidate for further genetic dissection.
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Affiliation(s)
- Calum Watt
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Lee-Anne McFawn
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
| | | | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia.
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia.
- Department of Primary Industry and Regional Development, Perth, WA, Australia.
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Fast mapping of a chlorophyll b synthesis-deficiency gene in barley (Hordeum vulgare L.) via bulked-segregant analysis with reduced-representation sequencing. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ali I, Teng Z, Bai Y, Yang Q, Hao Y, Hou J, Jia Y, Tian L, Liu X, Tan Z, Wang W, Kenneth K, Sharkh AYA, Liu D, Guo K, Zhang J, Liu D, Zhang Z. A high density SLAF-SNP genetic map and QTL detection for fibre quality traits in Gossypium hirsutum. BMC Genomics 2018; 19:879. [PMID: 30522437 PMCID: PMC6282304 DOI: 10.1186/s12864-018-5294-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
Background Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome for single nucleotide polymorphism marker identification and high density genetic map construction toward more reliable quantitative trait locus mapping. Results In the present study, a RIL population was developed by crossing a Chinese high fiber quality cultivar (Yumian 1) and an American high fiber quality line (CA3084), with distinct genetic backgrounds. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to discover SNPs, and a genetic map containing 6254 SNPs was constructed, covering 3141.72 cM with an average distance of 0.5 cM between markers. A total of 95 QTL were detected for fiber quality traits in three environments, explaining 5.5-24.6% of the phenotypic variance. Fifty-five QTL found in multiple environments were considered stable QTL. Nine of the stable QTL were found in all three environments. We identified 14 QTL clusters on 13 chromosomes, each containing one or more stable QTL. Conclusion A high-density genetic map of Gossypium hirsutum developed by using specific locus amplified fragment sequencing technology provides detailed mapping of fiber quality QTL, and identification of ‘stable QTL’ found in multiple environments. A marker-rich genetic map provides a foundation for fine mapping, candidate gene identification and marker-assisted selection of favorable alleles at stable QTL in breeding programs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5294-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Iftikhar Ali
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Zhonghua Teng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yuting Bai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Qing Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yongshui Hao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Juan Hou
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yongbin Jia
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Lixia Tian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Zhaoyun Tan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Kiirya Kenneth
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | | | - Dexin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Dajun Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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Liu L, Luo Q, Li H, Li B, Li Z, Zheng Q. Physical mapping of the blue-grained gene from Thinopyrum ponticum chromosome 4Ag and development of blue-grain-related molecular markers and a FISH probe based on SLAF-seq technology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2359-2370. [PMID: 30128741 DOI: 10.1007/s00122-018-3158-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/03/2018] [Indexed: 05/09/2023]
Abstract
A Thinopyrum ponticum chromosome 4Ag physical map was constructed, the blue-grained gene was localized, and related specific markers and a FISH probe were developed by SLAF-seq. Decaploid Thinopyrum ponticum (2n = 10x = 70) serves as an important gene pool for wheat improvement. The wheat-Th. ponticum 4Ag (4D) disomic substitution line Blue 58, derived from a distant hybridization between Th. ponticum and common wheat (Triticum aestivum L.), bears blue coloration in the aleurone layer. To map the blue-grained gene, eight wheat-Th. ponticum 4Ag translocation lines with different chromosomal segment sizes were obtained from Blue 58 using 60Co-γ ray irradiation and were characterized using cytogenetic and molecular marker analysis. A small-segment blue-grained wheat translocation line L13, accounting for one-fifth of 4AgL, was obtained. A physical map of chromosome 4Ag was constructed containing 573 specific-locus amplified fragment sequencing (SLAF-seq) markers, including three bins with 223 markers on 4AgS and eight bins with 350 markers on 4AgL. The blue-grained gene in three blue-grained translocation lines L5, L9, and L13, was located on bin 4AgL-6 with FL 0.75-0.89. Moreover, 89 blue-grain-related molecular markers and one fluorescence in situ hybridization (FISH) probe, pThp12.19, were identified in this bin. The newly developed translocation lines and the molecular markers and FISH probe will facilitate the application of the Th. ponticum-origin blue-grained characteristic in wheat breeding.
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Affiliation(s)
- Liqin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Liu L, Luo Q, Teng W, Li B, Li H, Li Y, Li Z, Zheng Q. Development of Thinopyrum ponticum-specific molecular markers and FISH probes based on SLAF-seq technology. PLANTA 2018; 247:1099-1108. [PMID: 29356894 DOI: 10.1007/s00425-018-2845-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/07/2018] [Indexed: 05/06/2023]
Abstract
Based on SLAF-seq, 67 Thinopyrum ponticum-specific markers and eight Th. ponticum-specific FISH probes were developed, and these markers and probes could be used for detection of alien chromatin in a wheat background. Decaploid Thinopyrum ponticum (2n = 10x = 70) is a valuable gene reservoir for wheat improvement. Identification of Th. ponticum introgression would facilitate its transfer into diverse wheat genetic backgrounds and its practical utilization in wheat improvement. Based on specific-locus-amplified fragment sequencing (SLAF-seq) technology, 67 new Th. ponticum-specific molecular markers and eight Th. ponticum-specific fluorescence in situ hybridization (FISH) probes have been developed from a tiny wheat-Th. ponticum translocation line. These newly developed molecular markers allowed the detection of Th. ponticum DNA in a variety of materials specifically and steadily at high throughput. According to the hybridization signal pattern, the eight Th. ponticum-specific probes could be divided into two groups. The first group including five dispersed repetitive sequence probes could identify Th. ponticum chromatin more sensitively and accurately than genomic in situ hybridization (GISH). Whereas the second group having three tandem repetitive sequence probes enabled the discrimination of Th. ponticum chromosomes together with another clone pAs1 in wheat-Th. ponticum partial amphiploid Xiaoyan 68.
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Affiliation(s)
- Liqin Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Qiaoling Luo
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wan Teng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Bin Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Hongwei Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Yiwen Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China
| | - Zhensheng Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China.
| | - Qi Zheng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences/State Key Laboratory of Plant Cell and Chromosome Engineering, Beijing, 100101, China.
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Rapid identification of a stripe rust resistant gene in a space-induced wheat mutant using specific locus amplified fragment (SLAF) sequencing. Sci Rep 2018; 8:3086. [PMID: 29449594 PMCID: PMC5814476 DOI: 10.1038/s41598-018-21489-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 02/06/2018] [Indexed: 11/08/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat. Resistant cultivars are the preferred strategy to control the disease. Space-induced wheat mutant R39 has adult-plant resistance (APR) to Pst. Genetic analysis indicated that a single recessive gene, designated YrR39, was responsible for the APR of R39 to Pst. Bulked segregant analysis (BSA) combined with a SLAF sequencing (SLAF-seq) strategy was used to fine-map YrR39 to a 17.39 Mb segment on chromosome 4B. The region was confirmed by analysis with simple sequence repeat (SSR) markers. A total of 126 genes were annotated in the region and 21 genes with annotations associated with disease response were selected for further qRT-PCR analysis. The candidate gene Traes_4BS_C868349E1 (annotated as an F-box/LRR-repeat protein) was up-regulated after 12, 24, 48, and 96 hours post inoculation with Pst, suggesting it is likely involved in the resistance. The current study demonstrated that BSA combined with SLAF-seq for SNP discovery is an efficient approach for mapping and identifying candidate functional gene.
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Braumann I, Dockter C, Beier S, Himmelbach A, Lok F, Lundqvist U, Skadhauge B, Stein N, Zakhrabekova S, Zhou R, Hansson M. Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding. Hereditas 2017; 155:10. [PMID: 28878591 PMCID: PMC5583965 DOI: 10.1186/s41065-017-0045-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Short-culm mutants have been widely used in breeding programs to increase lodging resistance. In barley (Hordeum vulgare L.), several hundreds of short-culm mutants have been isolated over the years. The objective of the present study was to identify the Brachytic1 (Brh1) semi-dwarfing gene and to test its effect on yield and malting quality. RESULTS Double-haploid lines generated through a cross between a brh1.a mutant and the European elite malting cultivar Quench, showed good malting quality but a decrease in yield. Especially the activities of the starch degrading enzymes β-amylase and free limit dextrinase were high. A syntenic approach comparing markers in barley to those in rice (Oryza sativa L.), sorghum (Sorghum bicolor Moench) and brachypodium (Brachypodium distachyon P. Beauv) helped us to identify Brh1 as an orthologue of rice D1 encoding the Gα subunit of a heterotrimeric G protein. We demonstrated that Brh1 is allelic to Ari-m. Sixteen different mutant alleles were described at the DNA level. CONCLUSIONS Mutants in the Brh1 locus are deficient in the Gα subunit of a heterotrimeric G protein, which shows that heterotrimeric G proteins are important regulators of culm length in barley. Mutant alleles do not have any major negative effects on malting quality.
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Affiliation(s)
- Ilka Braumann
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Finn Lok
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Smedjevägen 3, SE-23053 Alnarp, Sweden
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | | | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, SE-22362 Lund, Sweden
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Cao D, Lutz A, Hill CB, Callahan DL, Roessner U. A Quantitative Profiling Method of Phytohormones and Other Metabolites Applied to Barley Roots Subjected to Salinity Stress. FRONTIERS IN PLANT SCIENCE 2017; 7:2070. [PMID: 28119732 PMCID: PMC5222860 DOI: 10.3389/fpls.2016.02070] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/27/2016] [Indexed: 05/22/2023]
Abstract
As integral parts of plant signaling networks, phytohormones are involved in the regulation of plant metabolism and growth under adverse environmental conditions, including salinity. Globally, salinity is one of the most severe abiotic stressors with an estimated 800 million hectares of arable land affected. Roots are the first plant organ to sense salinity in the soil, and are the initial site of sodium (Na+) exposure. However, the quantification of phytohormones in roots is challenging, as they are often present at extremely low levels compared to other plant tissues. To overcome this challenge, we developed a high-throughput LC-MS method to quantify ten endogenous phytohormones and their metabolites of diverse chemical classes in roots of barley. This method was validated in a salinity stress experiment with six barley varieties grown hydroponically with and without salinity. In addition to phytohormones, we quantified 52 polar primary metabolites, including some phytohormone precursors, using established GC-MS and LC-MS methods. Phytohormone and metabolite data were correlated with physiological measurements including biomass, plant size and chlorophyll content. Root and leaf elemental analysis was performed to determine Na+ exclusion and K+ retention ability in the studied barley varieties. We identified distinct phytohormone and metabolite signatures as a response to salinity stress in different barley varieties. Abscisic acid increased in the roots of all varieties under salinity stress, and elevated root salicylic acid levels were associated with an increase in leaf chlorophyll content. Furthermore, the landrace Sahara maintained better growth, had lower Na+ levels and maintained high levels of the salinity stress linked metabolite putrescine as well as the phytohormone metabolite cinnamic acid, which has been shown to increase putrescine concentrations in previous studies. This study highlights the importance of root phytohormones under salinity stress and the multi-variety analysis provides an important update to analytical methodology, and adds to the current knowledge of salinity stress responses in plants at the molecular level.
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Affiliation(s)
- Da Cao
- School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
| | - Adrian Lutz
- Metabolomics Australia, School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
| | - Camilla B. Hill
- School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
- School of Veterinary and Life Sciences, Murdoch University, MurdochWA, Australia
| | - Damien L. Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, BurwoodVIC, Australia
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
- Metabolomics Australia, School of BioSciences, The University of Melbourne, ParkvilleVIC, Australia
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