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Singh CK, Singh D, Sharma S, Chandra S, Tomar RSS, Kumar A, Upadhyaya KC, Pal M. Mechanistic Association of Quantitative Trait Locus with Malate Secretion in Lentil ( Lens culinaris Medikus) Seedlings under Aluminium Stress. PLANTS 2021; 10:plants10081541. [PMID: 34451586 PMCID: PMC8400473 DOI: 10.3390/plants10081541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 12/04/2022]
Abstract
Aluminium (Al) toxicity acts as a major delimiting factor in the productivity of many crops including lentil. To alleviate its effect, plants have evolved with Al exclusion and inclusion mechanisms. The former involves the exudation of organic acid to restrict the entry of Al3+ to the root cells while latter involves detoxification of entered Al3+ by organic acids. Al-induced secretion of organic acids from roots is a well-documented mechanism that chelates and neutralizes Al3+ toxicity. In this study, F6 recombinant inbred lines (RILs) derived from a cross between L-7903 (Al-resistant) and BM-4 (Al-sensitive) were phenotyped to assess variation in secretion levels of malate and was combined with genotypic data obtained from 10 Al-resistance linked simple sequence repeat (SSRs) markers. A major quantitative trait loci (QTL) was mapped for malate (qAlt_ma) secretion with a logarithm of odd (LOD) value of 7.7 and phenotypic variation of 60.2%.Validated SSRs associated with this major QTL will be useful in marker assisted selection programmes for improving Al resistance in lentil.
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Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (C.K.S.); (S.S.)
- Amity Institute of Biotechnology, Amity University, Noida 201313, India;
| | - Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (C.K.S.); (S.S.)
- Correspondence: (D.S.); (M.P.); Tel.: +91-7011180774 (D.S.); +91-9868783354 (M.P.)
| | - Shristi Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (C.K.S.); (S.S.)
| | - Shivani Chandra
- Amity Institute of Biotechnology, Amity University, Noida 201313, India;
| | - Ram Sewak Singh Tomar
- ICAR-National Institute of Plant Biotechnology, Pusa Campus, New Delhi 110012, India;
| | - Arun Kumar
- National Phytotron Facility, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - K. C. Upadhyaya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India
- Correspondence: (D.S.); (M.P.); Tel.: +91-7011180774 (D.S.); +91-9868783354 (M.P.)
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Ambachew D, Blair MW. Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean ( Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity. FRONTIERS IN PLANT SCIENCE 2021; 12:628687. [PMID: 34249030 PMCID: PMC8269929 DOI: 10.3389/fpls.2021.628687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/13/2021] [Indexed: 06/13/2023]
Abstract
Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed.
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Farokhzadeh S, Fakheri BA, Nezhad NM, Tahmasebi S, Mirsoleimani A, Lynne McIntyre C. Genetic control of some plant growth characteristics of bread wheat (Triticum aestivum L.) under aluminum stress. Genes Genomics 2019; 42:245-261. [PMID: 31833049 DOI: 10.1007/s13258-019-00895-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/21/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Biomass yield is an important trait for wheat breeding programs. Enhancing the yield of the aerial components of wheat cultivars will be an integral part of future wheat improvement. Aluminum (Al) toxicity is one of the main factors limiting wheat growth and production in acid soils, which occur on up to 50% of the arable lands of the world especially in tropical and subtropical regions. OBJECTIVE Our objective was to identify quantitative trait loci (QTL) of plant growth characteristics and yield in wheat. METHODS A recombinant inbred line (RIL) population consisting of 167 lines, derived from a cross between SeriM82 and Babax were evaluated under two Al treatments (+ Al, 800 µM of Al; -Al, 0 µM of Al) in the field based on an alpha lattice design with two replications for two consecutive crop seasons. RESULTS A total of 40 QTLs including nine putative and 31 suggestive QTLs were found for all traits using the composite interval mapping (CIM) method. By mixed model-based composite interval mapping (MCIM) method, 42 additive QTLs and nine pairs of epistatic effects were detected for studied traits, of which 20 additive and six pairs of epistatic QTLs showed significant QTL × environment interactions. Most of the detected QTLs across environments were stable, and the highest number of stable QTLs was related to A genome. Co-localization of QTL was found on linkage groups (LGs) 2B, 4B, 6A-a, and 7A (CIM method) and 2A-d, and 6A-a (MCIM method). CONCLUSION These results have implications for selection strategies in biomass yield and for increasing the yield of the aerial part of wheat following further evaluations in various genetic backgrounds and environments.
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Affiliation(s)
- Sara Farokhzadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Bonjar Rd, Zabol, Sistan and Baluchestan provice, Iran.
| | - Barat Ali Fakheri
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Bonjar Rd, Zabol, Sistan and Baluchestan provice, Iran
| | - Nafiseh Mahdi Nezhad
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Bonjar Rd, Zabol, Sistan and Baluchestan provice, Iran
| | - Sirous Tahmasebi
- Department of Seed and Plant Improvement Research, Fars Agriculture and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz, Iran.
| | - Abbas Mirsoleimani
- Department of Plant Production, Faculty of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | - C Lynne McIntyre
- CSIRO Agriculture, Queensl and Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
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Genome Wide Association Study of Karnal Bunt Resistance in a Wheat Germplasm Collection from Afghanistan. Int J Mol Sci 2019; 20:ijms20133124. [PMID: 31247965 PMCID: PMC6651844 DOI: 10.3390/ijms20133124] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/23/2019] [Accepted: 06/25/2019] [Indexed: 01/22/2023] Open
Abstract
Karnal bunt disease of wheat, caused by the fungus Neovossia indica, is one of the most important challenges to the grain industry as it affects the grain quality and also restricts the international movement of infected grain. It is a seed-, soil- and airborne disease with limited effect of chemical control. Currently, this disease is contained through the deployment of host resistance but further improvement is limited as only a few genotypes have been found to carry partial resistance. To identify genomic regions responsible for resistance in a set of 339 wheat accessions, genome-wide association study (GWAS) was undertaken using the DArTSeq® technology, in which 18 genomic regions for Karnal bunt resistance were identified, explaining 5–20% of the phenotypic variation. The identified quantitative trait loci (QTL) on chromosome 2BL showed consistently significant effects across all four experiments, whereas another QTL on 5BL was significant in three experiments. Additional QTLs were mapped on chromosomes 1DL, 2DL, 4AL, 5AS, 6BL, 6BS, 7BS and 7DL that have not been mapped previously, and on chromosomes 4B, 5AL, 5BL and 6BS, which have been reported in previous studies. Germplasm with less than 1% Karnal bunt infection have been identified and can be used for resistance breeding. The SNP markers linked to the genomic regions conferring resistance to Karnal bunt could be used to improve Karnal bunt resistance through marker-assisted selection.
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Unravelling the Complex Genetics of Karnal Bunt ( Tilletia indica) Resistance in Common Wheat ( Triticum aestivum) by Genetic Linkage and Genome-Wide Association Analyses. G3-GENES GENOMES GENETICS 2019; 9:1437-1447. [PMID: 30824480 PMCID: PMC6505162 DOI: 10.1534/g3.119.400103] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Karnal bunt caused by Tilletia indica Mitra [syn. Neovossia indica (Mitra) Mundkur] is a significant biosecurity concern for wheat-exporting countries that are free of the disease. It is a seed-, soil-and air-borne disease with no effective chemical control measures. The current study used data from multi-year field experiments of two bi-parental populations and a genome-wide association (GWA) mapping panel to unravel the genetic basis for resistance in common wheat. Broad-sense heritability for Karnal bunt resistance in the populations varied from 0.52 in the WH542×HD29 population, to 0.61 in the WH542×W485 cross and 0.71 in a GWAS panel. Quantitative trait locus (QTL) analysis with seven years of phenotypic data identified a major locus on chromosome 3B (R2 = 27.8%) and a minor locus on chromosome 1A (R2 = 12.2%), in the WH542×HD29 population, with both parents contributing the high-value alleles. A major locus (R2 = 27.8%) and seven minor loci (R2 = 4.4–15.8%) were detected in the WH542×W485 population. GWA mapping validated QTL regions in the bi-parent populations, but also identified novel loci not previously associated with Karnal bunt resistance. Meta-QTL analysis aligned the results from this study with those reported in wheat over the last two decades. Two major clusters were detected, the first on chromosome 4B, which clustered with Qkb.ksu-4B, QKb.cimmyt-4BL, Qkb.cim-4BL, and the second on chromosome 3B, which clustered with Qkb.cnl-3B, QKb.cimmyt-3BS and Qkb.cim-3BS1. The results provide definitive chromosomal assignments for QTL/genes controlling Karnal bunt resistance in common wheat, and will be useful in pre-emptive breeding against the pathogen in wheat-producing areas that are free of the disease.
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Jing Y, Zhao X, Wang J, Teng W, Qiu L, Han Y, Li W. Identification of the Genomic Region Underlying Seed Weight per Plant in Soybean ( Glycine max L. Merr.) via High-Throughput Single-Nucleotide Polymorphisms and a Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2018; 9:1392. [PMID: 30369935 PMCID: PMC6194254 DOI: 10.3389/fpls.2018.01392] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/03/2018] [Indexed: 05/30/2023]
Abstract
Seed weight per plant (SWPP) of soybean (Glycine max (L.) Merr.), a complicated quantitative trait controlled by multiple genes, was positively associated with soybean seed yields. In the present study, a natural soybean population containing 185 diverse accessions primarily from China was used to analyze the genetic basis of SWPP via genome-wide association analysis (GWAS) based on high-throughput single-nucleotide polymorphisms (SNPs) generated by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) method. A total of 33,149 SNPs were finally identified with minor allele frequencies (MAF) > 5% which were present in 97% of all the genotypes. Twenty association signals associated with SWPP were detected via GWAS. Among these signals, eight SNPs were novel loci, and the other twelve SNPs were overlapped or located in the linked genomic regions of the reported QTL from SoyBase database. Several genes belonging to the categories of hormone pathways, RNA regulation of transcription in plant development, ubiquitin, transporting systems, and other metabolisms were considered as candidate genes associated with SWPP. Furthermore, nine genes from the flanking region of Gm07:19488264, Gm08:15768591, Gm08:15768603, or Gm18:23052511 were significantly associated with SWPP and were stable among multiple environments. Nine out of 18 haplotypes from nine genes showed the effect of increasing SWPP. The identified loci along with the beneficial alleles and candidate genes could be of great value for studying the molecular mechanisms underlying SWPP and for improving the potential seed yield of soybean in the future.
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Affiliation(s)
- Yan Jing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Jinyang Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
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Garcia-Oliveira AL, Benito C, Guedes-Pinto H, Martins-Lopes P. Molecular cloning of TaMATE2 homoeologues potentially related to aluminium tolerance in bread wheat (Triticum aestivum L.). PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:817-824. [PMID: 29908003 DOI: 10.1111/plb.12864] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Recently, members of the MATE family have been implicated in aluminium (Al) tolerance by facilitating citrate efflux in plants. The aim of the present work was to perform a molecular characterisation of the MATE2 gene in bread wheat. Here, we cloned a member of the MATE gene family in bread wheat and named it TaMATE2, which showed the typical secondary structure of MATE-type transporters maintaining all the 12 transmembrane domains. Amplification in Chinese Spring nulli-tetrasomic and ditelosomic lines revealed that TaMATE2 is located on the long arm of homoeologous group 1 chromosomes. The transcript expression of TaMATE2 homoeologues in two diverse bread wheat genotypes, Barbela 7/72/92 (Al-tolerant) and Anahuac (Al-sensitive), suggested that TaMATE2 is expressed in both root and shoot tissues of bread wheat, but mainly confined to root rather than shoot tissues. A time-course analysis of TaMATE2 homoeologue transcript expression revealed the Al responsive expression of TaMATE2 in root apices of the Al-tolerant genotype, Barbela 7/72/92. Considering the high similarity of TaMATE2 together with similar Al responsive expression pattern as of ScFRDL2 from rye and OsFRDL2 from rice, it is likely that TaMATE2 also encodes a citrate transporter. Furthermore, the TaMATE2-D homoeologue appears to be near the previously reported locus (wPt0077) on chromosome 1D for Al tolerance. In conclusion, molecular cloning of TaMATE2 homoeologues, particularly TaMATE2-D, provides a plausible candidate for Al tolerance in bread wheat that can be used for the development of more Al-tolerant cultivars in this staple crop.
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Affiliation(s)
- A L Garcia-Oliveira
- Department of Genetics, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - C Benito
- Department of Genetics, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - H Guedes-Pinto
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - P Martins-Lopes
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
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Jighly A, Joukhadar R, Singh S, Ogbonnaya FC. Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat. Front Genet 2018; 9:27. [PMID: 29467793 PMCID: PMC5807918 DOI: 10.3389/fgene.2018.00027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/22/2018] [Indexed: 11/13/2022] Open
Abstract
Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes) with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding.
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Affiliation(s)
- Abdulqader Jighly
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Reem Joukhadar
- Agriculture Victoria, Agriculture Research Division, AgriBio, Centre for AgriBiosciences, Bundoora, VIC, Australia.,Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Tadele Z. African Orphan Crops under Abiotic Stresses: Challenges and Opportunities. SCIENTIFICA 2018; 2018:1451894. [PMID: 29623231 PMCID: PMC5829434 DOI: 10.1155/2018/1451894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/17/2017] [Indexed: 05/23/2023]
Abstract
A changing climate, a growing world population, and a reduction in arable land devoted to food production are all problems facing the world food security. The development of crops that can yield under uncertain and extreme climatic and soil growing conditions can play a key role in mitigating these problems. Major crops such as maize, rice, and wheat are responsible for a large proportion of global food production but many understudied crops (commonly known as "orphan crops") including millets, cassava, and cowpea feed millions of people in Asia, Africa, and South America and are already adapted to the local environments in which they are grown. The application of modern genetic and genomic tools to the breeding of these crops can provide enormous opportunities for ensuring world food security but is only in its infancy. In this review, the diversity and types of understudied crops will be introduced, and the beneficial traits of these crops as well as their role in the socioeconomics of Africa will be discussed. In addition, the response of orphan crops to diverse types of abiotic stresses is investigated. A review of the current tools and their application to the breeding of enhanced orphan crops will also be described. Finally, few examples of global efforts on tackling major abiotic constraints in Africa are presented.
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Affiliation(s)
- Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Center for Development and Environment (CDE), University of Bern, Bern, Switzerland
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
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Sadhukhan A, Kobayashi Y, Nakano Y, Iuchi S, Kobayashi M, Sahoo L, Koyama H. Genome-wide Association Study Reveals that the Aquaporin NIP1;1 Contributes to Variation in Hydrogen Peroxide Sensitivity in Arabidopsis thaliana. MOLECULAR PLANT 2017; 10:1082-1094. [PMID: 28712931 DOI: 10.1016/j.molp.2017.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 06/25/2017] [Accepted: 07/03/2017] [Indexed: 05/27/2023]
Abstract
Hydrogen peroxide (H2O2) is a reactive oxygen species that affects cell signaling in various plant defense responses and induces programmed cell death. To identify the new components associated with H2O2 signaling and tolerance, we conducted a genome-wide association study (GWAS) on the root growth of 133 Arabidopsis thaliana accessions grown in the presence of toxic H2O2 levels. The most significant SNPs were associated with a cluster of chromosome 4 genes encoding an aquaporin NODULIN 26-LIKE INTRINSIC PROTEIN 1; 1 (NIP1;1), an NB-ARC domain-containing disease resistance protein (AT4G19050), and a putative membrane lipoprotein (AT4G19070). The expression level of NIP1;1 was relatively high in A. thaliana accessions sensitive to H2O2. Additionally, overexpression of NIP1;1 in a tolerant accession (e.g., Col-0) increased the sensitivity of transgenic plants to H2O2. An in planta β-glucuronidase reporter assay revealed that variations in the NIP1;1 promoter were responsible for the differences of its expression level in H2O2-tolerant and -sensitive accessions. Cell death was extensive and H2O2 levels were high in the roots of H2O2-sensitive and NIP1;1-overexpressing accessions. Together, our results indicate that the aquaporin NIP1;1 is a key determinant of the sensitivity of A. thaliana to H2O2, and contributes to the phenotypic variations detected by our GWAS.
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Affiliation(s)
- Ayan Sadhukhan
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Yuriko Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Yuki Nakano
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Satoshi Iuchi
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masatomo Kobayashi
- Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Lingaraj Sahoo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Hiroyuki Koyama
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
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Zhao X, Teng W, Li Y, Liu D, Cao G, Li D, Qiu L, Zheng H, Han Y, Li W. Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7. BMC Genomics 2017; 18:462. [PMID: 28615053 PMCID: PMC5471737 DOI: 10.1186/s12864-017-3843-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/05/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Soybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim of the present study was to investigate the genome-wide genetic architecture of resistance to SCN HG Type 2.5.7 (race 1) in landrace and elite cultivated soybeans. RESULTS A total of 200 diverse soybean accessions were screened for resistance to SCN HG Type 2.5.7 and genotyped through sequencing using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach with a 6.14-fold average sequencing depth. A total of 33,194 SNPs were identified with minor allele frequencies (MAF) over 4%, covering 97% of all the genotypes. Genome-wide association mapping (GWAS) revealed thirteen SNPs associated with resistance to SCN HG Type 2.5.7. These SNPs were distributed on five chromosomes (Chr), including Chr7, 8, 14, 15 and 18. Four SNPs were novel resistance loci and nine SNPs were located near known QTL. A total of 30 genes were identified as candidate genes underlying SCN resistance. CONCLUSIONS A total of sixteen novel soybean accessions were identified with significant resistance to HG Type 2.5.7. The beneficial alleles and candidate genes identified by GWAS might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying SCN resistance.
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Affiliation(s)
- Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Yinghui Li
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dongyuan Liu
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300 China
| | - Guanglu Cao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Dongmei Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300 China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
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Liu Z, Li H, Fan X, Huang W, Yang J, Wen Z, Li Y, Guan R, Guo Y, Chang R, Wang D, Chen P, Wang S, Qiu LJ. Phenotypic characterization and genetic dissection of nine agronomic traits in Tokachi nagaha and its derived cultivars in soybean (Glycine max (L.) Merr.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 256:72-86. [PMID: 28167041 DOI: 10.1016/j.plantsci.2016.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/20/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
By using the soybean founder parent Tokachi nagaha and its 137 derived cultivars as materials, a genome-wide association analysis was performed to identify the single nucleotide polymorphisms (SNPs) underlying soybean yield and quality related traits at two planting densities. Results of ANOVA showed that genotype, environment, and genotype by environment interaction effects were all significant for each trait. The Tokachi nagaha-derived soybean population could be divided into two subpopulations based on molecular data, and accessions in each subpopulation were almost all from the same Chinese province. Relatedness was detected between pair-wise accessions within the population. Linkage disequilibrium was obvious and the level of intra-chromosome linkage disequilibrium was about 8370kb. A total of 40 SNPs with significant signal were detected and distributed across 18 chromosomes. Some SNP markers were located in or near regions where QTLs have been previously mapped by linkage analysis. Nineteen SNPs were identified both in low- and high- density planting treatments, indicating those loci were common and sTable Sixteen SNPs were co-associated with two or more different traits, suggesting that some of the QTLs/genes underlying those identified SNPs were likely to be pleiotropic.
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Affiliation(s)
- Zhangxiong Liu
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Huihui Li
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Xuhong Fan
- Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun 130124, China.
| | - Wen Huang
- Tonghua Academy of Agricultural Sciences, Meihekou 135007, China.
| | - Jiyu Yang
- Jilin City Academy of Agricultural Sciences, Jilin 132101, China.
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, USA.
| | - Yinghui Li
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Rongxia Guan
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Yong Guo
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Ruzhen Chang
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, USA.
| | - Pengyin Chen
- Department of Crop, Soil and Environment Sciences, University of Arkansas, Fayetteville 72701, USA.
| | - Shuming Wang
- Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun 130124, China.
| | - Li-Juan Qiu
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing 100081, China.
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Aguilera JG, Minozzo JAD, Barichello D, Fogaça CM, da Silva JP, Consoli L, Pereira JF. Alleles of organic acid transporter genes are highly correlated with wheat resistance to acidic soil in field conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1317-1331. [PMID: 27008477 DOI: 10.1007/s00122-016-2705-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
TaALMT1 and TaMATE1B promoter alleles are highly correlated with wheat growth in acidic soil with a high concentration of toxic aluminium. The aluminium (Al(3+)) resistance of 338 wheat genotypes with different geographic origins was correlated with morphological traits and TaALMT1 and TaMATE1B alleles. Both of these genes encode malate and citrate transporters associated with Al(3+) resistance mechanisms in wheat. Based on comparisons with the sensitive and resistant controls, the relative root growth was evaluated in hydroponic experiments and the plant performance was visually accessed in the field. The correlation between Al(3+) tolerance in the hydroponic and field tests was moderate (r = 0.56, P < 0.001). Higher selection pressure was observed in the field because a smaller number of genotypes was classified as resistant. The combination between the six TaALMT1 alleles and the two TaMATE1B promoters allowed the identification of 11 haplotypes that showed a high (r = 0.71, P < 0.001) correlation with Al(3+) resistance in the field, with the TaALMT1 alleles accounting for most of the correlation. The Brazilian wheat genotypes presented the best performance in soil, including eight cultivars with promoters usually associated with Al(3+) resistance and another six genotypes classified as moderately resistant but containing alleles usually associated with Al(3+) sensitivity. Although an increase in favourable alleles was observed over the past few decades, the average Al(3+) resistance in the field was not significantly different from that of older cultivars. The ease identification of the TaALMT1 and TaMATE1B alleles and their higher association with Al(3+) resistance along with the best genotypes identified here may be used for wheat-breeding programmes interested in increasing wheat Al(3+) resistance.
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Affiliation(s)
- Jorge G Aguilera
- Embrapa Trigo, Rodovia BR 285 km 294, Passo Fundo, RS, 99050-970, Brazil
| | - João A D Minozzo
- Embrapa Trigo, Rodovia BR 285 km 294, Passo Fundo, RS, 99050-970, Brazil
- Universidade de Passo Fundo, Rodovia BR 285, Passo Fundo, RS, 99052-900, Brazil
| | - Diliane Barichello
- Embrapa Trigo, Rodovia BR 285 km 294, Passo Fundo, RS, 99050-970, Brazil
- Instituto Agronômico do Paraná, Rodovia Celso Garcia Cid km 375, Londrina, PR, 86047-902, Brazil
| | - Claúdia M Fogaça
- Embrapa Trigo, Rodovia BR 285 km 294, Passo Fundo, RS, 99050-970, Brazil
- Fundação Estadual de Pesquisa Agropecuária, RSC 470 km 170, Veranópolis, RS, 95330-000, Brazil
| | | | - Luciano Consoli
- Embrapa Trigo, Rodovia BR 285 km 294, Passo Fundo, RS, 99050-970, Brazil
| | - Jorge F Pereira
- Embrapa Trigo, Rodovia BR 285 km 294, Passo Fundo, RS, 99050-970, Brazil
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Liu Z, Li H, Fan X, Huang W, Yang J, Li C, Wen Z, Li Y, Guan R, Guo Y, Chang R, Wang D, Wang S, Qiu LJ. Phenotypic Characterization and Genetic Dissection of Growth Period Traits in Soybean (Glycine max) Using Association Mapping. PLoS One 2016; 11:e0158602. [PMID: 27367048 PMCID: PMC4930185 DOI: 10.1371/journal.pone.0158602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/18/2016] [Indexed: 11/17/2022] Open
Abstract
The growth period traits are important traits that affect soybean yield. The insights into the genetic basis of growth period traits can provide theoretical basis for cultivated area division, rational distribution, and molecular breeding for soybean varieties. In this study, genome-wide association analysis (GWAS) was exploited to detect the quantitative trait loci (QTL) for number of days to flowering (ETF), number of days from flowering to maturity (FTM), and number of days to maturity (ETM) using 4032 single nucleotide polymorphism (SNP) markers with 146 cultivars mainly from Northeast China. Results showed that abundant phenotypic variation was presented in the population, and variation explained by genotype, environment, and genotype by environment interaction were all significant for each trait. The whole accessions could be clearly clustered into two subpopulations based on their genetic relatedness, and accessions in the same group were almost from the same province. GWAS based on the unified mixed model identified 19 significant SNPs distributed on 11 soybean chromosomes, 12 of which can be consistently detected in both planting densities, and 5 of which were pleotropic QTL. Of 19 SNPs, 7 SNPs located in or close to the previously reported QTL or genes controlling growth period traits. The QTL identified with high resolution in this study will enrich our genomic understanding of growth period traits and could then be explored as genetic markers to be used in genomic applications in soybean breeding.
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Affiliation(s)
- Zhangxiong Liu
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Huihui Li
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Xuhong Fan
- Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wen Huang
- Tonghua Academy of Agricultural Sciences, Meihekou, China
| | - Jiyu Yang
- Jilin City Academy of Agricultural Sciences, Jilin, China
| | - Candong Li
- Jiamusi Branch of Heilongjiang Agricultural Sciences, Jiamusi, China
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Yinghui Li
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Rongxia Guan
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Yong Guo
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Ruzhen Chang
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Shuming Wang
- Institute of Soybean Research, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Li-Juan Qiu
- National Key Facility for Gene Resources and Genetic Improvement, Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, China
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15
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Han C, Zhang P, Ryan PR, Rathjen TM, Yan Z, Delhaize E. Introgression of genes from bread wheat enhances the aluminium tolerance of durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:729-739. [PMID: 26747046 DOI: 10.1007/s00122-015-2661-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/14/2015] [Indexed: 05/24/2023]
Abstract
The aluminium tolerance of durum wheat was markedly enhanced by introgression of TaALMT1 and TaMATE1B from bread wheat. In contrast to bread wheat, TaMATE1B conferred greater aluminium tolerance than TaALMT1. Durum wheat (tetraploid AABB, Triticum turgidum) is a species that grows poorly on acid soils due to its sensitivity of Al(3+). By contrast, bread wheat (hexaploid AABBDD, T. aestivum) shows a large variation in Al(3+) tolerance which can be attributed to a major gene (TaALMT1) located on chromosome 4D as well as to other genes of minor effect such as TaMATE1B. Genotypic variation for Al(3+) tolerance in durum germplasm is small and the introgression of genes from bread wheat is one option for enhancing the ability of durum wheat to grow on acid soils. Introgression of a large fragment of the 4D chromosome previously increased the Al(3+) tolerance of durum wheat demonstrating the viability of transferring the TaALMT1 gene to durum wheat to increase its Al(3+) tolerance. Here, we used a ph1 (pairing homoeologous) mutant of durum wheat to introgress a small fragment of the 4D chromosome harboring the TaALMT1 gene. The size of the 4D chromosomal fragment introgressed into durum wheat was estimated by markers, fluorescence in situ hybridisation and real-time quantitative PCR. In a parallel strategy, we introgressed TaMATE1B from bread wheat into durum wheat using conventional crosses. Both genes separately increased the Al(3+) tolerance of durum wheat in both hydroponics and soil cultures. In contrast to bread wheat, the TaMATE1B gene was more effective than TaALMT1 in increasing the Al(3+) tolerance of durum wheat grown on acid soil.
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Affiliation(s)
- Chang Han
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia
- School of Agriculture and Technology, Zunyi Normal College, Zunyi, 563002, Guizhou, China
| | - Peng Zhang
- The University of Sydney, 107 Cobbitty Rd, Cobbitty, NSW, 2570, Australia
| | - Peter R Ryan
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - Tina M Rathjen
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia
| | - ZeHong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
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16
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Kochian LV, Piñeros MA, Liu J, Magalhaes JV. Plant Adaptation to Acid Soils: The Molecular Basis for Crop Aluminum Resistance. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:571-98. [PMID: 25621514 DOI: 10.1146/annurev-arplant-043014-114822] [Citation(s) in RCA: 429] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Aluminum (Al) toxicity in acid soils is a significant limitation to crop production worldwide, as approximately 50% of the world's potentially arable soil is acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring resistance to Al toxicity has been a focus of intense research interest in the decade since the last article on crop acid soil tolerance was published in this journal. An impressive amount of progress has been made during that time that has greatly increased our understanding of the diversity of Al resistance genes and mechanisms, how resistance gene expression is regulated and triggered by Al and Al-induced signals, and how the proteins encoded by these genes function and are regulated. This review examines the state of our understanding of the physiological, genetic, and molecular bases for crop Al tolerance, looking at the novel Al resistance genes and mechanisms that have been identified over the past ten years. Additionally, it examines how the integration of molecular and genetic analyses of crop Al resistance is starting to be exploited for the improvement of crop plants grown on acid soils via both molecular-assisted breeding and biotechnology approaches.
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Affiliation(s)
- Leon V Kochian
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, New York 14853; , ,
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17
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Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Ruperao P, Parkin IAP, Batley J, Luckett DJ, Wratten N. Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS One 2014; 9:e101673. [PMID: 25006804 PMCID: PMC4090071 DOI: 10.1371/journal.pone.0101673] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 06/02/2014] [Indexed: 12/18/2022] Open
Abstract
Resistance to pod shattering (shatter resistance) is a target trait for global rapeseed (canola, Brassica napus L.), improvement programs to minimise grain loss in the mature standing crop, and during windrowing and mechanical harvest. We describe the genetic basis of natural variation for shatter resistance in B. napus and show that several quantitative trait loci (QTL) control this trait. To identify loci underlying shatter resistance, we used a novel genotyping-by-sequencing approach DArT-Seq. QTL analysis detected a total of 12 significant QTL on chromosomes A03, A07, A09, C03, C04, C06, and C08; which jointly account for approximately 57% of the genotypic variation in shatter resistance. Through Genome-Wide Association Studies, we show that a large number of loci, including those that are involved in shattering in Arabidopsis, account for variation in shatter resistance in diverse B. napus germplasm. Our results indicate that genetic diversity for shatter resistance genes in B. napus is limited; many of the genes that might control this trait were not included during the natural creation of this species, or were not retained during the domestication and selection process. We speculate that valuable diversity for this trait was lost during the natural creation of B. napus. To improve shatter resistance, breeders will need to target the introduction of useful alleles especially from genotypes of other related species of Brassica, such as those that we have identified.
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Affiliation(s)
- Harsh Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Rosy Raman
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Frank Detering
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Bruce, ACT, Australia
| | - Neil Coombes
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Simon Diffey
- University of Wollongong, Wollongong, NSW, Australia
| | - Gururaj Kadkol
- NSW Department of Primary Industries, Tamworth Agricultural Institute, Tamworth, NSW, Australia
| | - David Edwards
- Australian Centre for Plant Functional Genomic, School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia; School of Plant Biology, University of Western Australia, Perth, WA, Australia
| | | | - Pradeep Ruperao
- Australian Centre for Plant Functional Genomic, School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia; International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India
| | | | - Jacqueline Batley
- School of Plant Biology, University of Western Australia, Perth, WA, Australia; School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD, Australia
| | - David J Luckett
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Neil Wratten
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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Emebiri LC. Genetic variation and possible SNP markers for breeding wheat with low-grain asparagine, the major precursor for acrylamide formation in heat-processed products. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:1422-1429. [PMID: 24122675 DOI: 10.1002/jsfa.6434] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/16/2013] [Accepted: 10/04/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND In products made from wheat (Triticum aestivum) flour, acrylamide formation is almost exclusively determined by the level of free asparagine in the grain. Genetic variability for grain asparagine content was evaluated in order to assess the potential for acrylamide mitigation by breeding. RESULTS Free asparagine levels in the grains of 92 varieties varied from 137 to 471 mg kg⁻¹, representing an approximate threefold difference between the low- and high-asparagine genotypes. Heritability was low, with a value of 32%, indicating that breeding cultivars with inherently low grain asparagine would be a challenge. A genome-wide scan with single-nucleotide polymorphism (SNP) markers identified nine SNPs that were significantly (P < 0.001) associated with variation in free asparagine. The significant SNPs were localized on chromosome 5A, and explained between 14% and 24% of the observed variation. These putative SNPs are candidates for further studies to develop molecular markers. CONCLUSION Significant genetic variation exists for reducing acrylamide precursors in wheat flour, indicating that breeding and genetics could play an important role in mitigating the acrylamide risk in wheat products. The study identified a region on chromosome 5A that could provide a basis for further research to develop functional markers.
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Affiliation(s)
- Livinus C Emebiri
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, 2650, Australia
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Garcia-Oliveira AL, Benito C, Prieto P, de Andrade Menezes R, Rodrigues-Pousada C, Guedes-Pinto H, Martins-Lopes P. Molecular characterization of TaSTOP1 homoeologues and their response to aluminium and proton (H(+)) toxicity in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2013; 13:134. [PMID: 24034075 PMCID: PMC3848728 DOI: 10.1186/1471-2229-13-134] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 08/01/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Aluminium (Al) toxicity is considered to be one of the major constraints affecting crop productivity on acid soils. Being a trait governed by multiple genes, the identification and characterization of novel transcription factors (TFs) regulating the expression of entire response networks is a very promising approach. Therefore, the aim of the present study was to clone, localize, and characterize the TaSTOP1 gene, which belongs to the zinc finger family (Cys2His2 type) transcription factor, at molecular level in bread wheat. RESULTS TaSTOP1 loci were cloned and localized on the long arm of homoeologous group 3 chromosomes [3AL (TaSTOP1-A), 3BL (TaSTOP1-B) and 3DL (TaSTOP1-D)] in bread wheat. TaSTOP1 showed four potential zinc finger domains and the homoeologue TaSTOP1-A exhibited transactivation activity in yeast. Expression profiling of TaSTOP1 transcripts identified the predominance of homoeologue TaSTOP1-A followed by TaSTOP1-D over TaSTOP1-B in root and only predominance of TaSTOP1-A in shoot tissues of two diverse bread wheat genotypes. Al and proton (H(+)) stress appeared to slightly modulate the transcript of TaSTOP1 homoeologues expression in both genotypes of bread wheat. CONCLUSIONS Physical localization of TaSTOP1 results indicated the presence of a single copy of TaSTOP1 on homoeologous group 3 chromosomes in bread wheat. The three homoeologues of TaSTOP1 have similar genomic structures, but showed biased transcript expression and different response to Al and proton (H(+)) toxicity. These results indicate that TaSTOP1 homoeologues may differentially contribute under Al or proton (H(+)) toxicity in bread wheat. Moreover, it seems that TaSTOP1-A transactivation potential is constitutive and may not depend on the presence/absence of Al at least in yeast. Finally, the localization of TaSTOP1 on long arm of homoeologous group 3 chromosomes and the previously reported major loci associated with Al resistance at chromosome 3BL, through QTL and genome wide association mapping studies suggests that TaSTOP1 could be a potential candidate gene for genomic assisted breeding for Al tolerance in bread wheat.
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Affiliation(s)
- Ana Luísa Garcia-Oliveira
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid 28040, Spain
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal
| | - César Benito
- Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid (UCM), Madrid 28040, Spain
| | - Pilar Prieto
- Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible (IAS, CSIC), Alameda del Obispo s/n., P.O. Box 4084, Córdoba 14080, Spain
| | | | | | - Henrique Guedes-Pinto
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal
| | - Paula Martins-Lopes
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal
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20
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Hu Z, Zhang H, Kan G, Ma D, Zhang D, Shi G, Hong D, Zhang G, Yu D. Determination of the genetic architecture of seed size and shape via linkage and association analysis in soybean (Glycine max L. Merr.). Genetica 2013; 141:247-54. [PMID: 23754189 DOI: 10.1007/s10709-013-9723-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
Abstract
Seed-size traits, which are controlled by multiple genes in soybean, play an important role in determining seed yield, quality and appearance. However, the molecular mechanisms controlling the size of soybean seeds remain unclear, and little research has been done to investigate these mechanisms. In this study, we performed a genetic analysis to determine the genetic architecture of soybean seed size and shape via linkage and association analyses. We used 184 recombinant inbred lines (RILs) and 219 cultivated soybean accessions to evaluate seed length, seed width and seed height as seed-size traits, and their ratios of these values as seed-shape traits. Our results showed that all six traits had high heritability ranging from 92.46 to 98.47 %. Linkage analysis in the RILs identified 12 quantitative traits loci (QTLs), with five of these QTLs being associated with seed size, five with seed shape and two with the two first principal components of our principal component analysis (PCA). Association analysis in the 219 accessions detected 41 single nucleotide polymorphism (SNP)-trait associations, with 20 of these SNPs being associated with seed-size traits, seven with seed-shape traits and 14 with the two first principal components of our PCA. This analysis reveals that seed-size and seed-shape may be controlled by different genetic factors. Our results provide a greater understanding of phenotypic structure and genetic architecture of soybean seed, and the QTLs detected in this study form a basis for future fine mapping, quantitative trait gene cloning and molecular breeding in soybean.
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Affiliation(s)
- Zhenbin Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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Increasing Food Production in Africa by Boosting the Productivity of Understudied Crops. AGRONOMY-BASEL 2012. [DOI: 10.3390/agronomy2040240] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Raman H, Raman R, Nelson MN, Aslam MN, Rajasekaran R, Wratten N, Cowling WA, Kilian A, Sharpe AG, Schondelmaier J. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res 2011; 19:51-65. [PMID: 22193366 PMCID: PMC3276259 DOI: 10.1093/dnares/dsr041] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia.
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Gurung S, Mamidi S, Bonman JM, Jackson EW, del Río LE, Acevedo M, Mergoum M, Adhikari TB. Identification of novel genomic regions associated with resistance to Pyrenophora tritici-repentis races 1 and 5 in spring wheat landraces using association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1029-41. [PMID: 21744229 DOI: 10.1007/s00122-011-1645-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/22/2011] [Indexed: 05/07/2023]
Abstract
Tan spot, caused by Pyrenophora tritici-repentis, is a major foliar disease of wheat worldwide. Host plant resistance is the best strategy to manage this disease. Traditionally, bi-parental mapping populations have been used to identify and map quantitative trait loci (QTL) affecting tan spot resistance in wheat. The association mapping (AM) could be an alternative approach to identify QTL based on linkage disequilibrium (LD) within a diverse germplasm set. In this study, we assessed resistance to P. tritici-repentis races 1 and 5 in 567 spring wheat landraces from the USDA-ARS National Small Grains Collection (NSGC). Using 832 diversity array technology (DArT) markers, QTL for resistance to P. tritici-repentis races 1 and 5 were identified. A linear model with principal components suggests that at least seven and three DArT markers were significantly associated with resistance to P. tritici-repentis races 1 and 5, respectively. The DArT markers associated with resistance to race 1 were detected on chromosomes 1D, 2A, 2B, 2D, 4A, 5B, and 7D and explained 1.3-3.1% of the phenotypic variance, while markers associated with resistance to race 5 were distributed on 2D, 6A and 7D, and explained 2.2-5.9% of the phenotypic variance. Some of the genomic regions identified in this study correspond to previously identified loci responsible for resistance to P. tritici-repentis, offering validation for our AM approach. Other regions identified were novel and could possess genes useful for resistance breeding. Some DArT markers associated with resistance to race 1 also were localized in the same regions of wheat chromosomes where QTL for resistance to yellow rust, leaf rust and powdery mildew, have been mapped previously. This study demonstrates that AM can be a useful approach to identify and map novel genomic regions involved in resistance to P. tritici-repentis.
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Affiliation(s)
- S Gurung
- Department of Plant Pathology, North Dakota State University, NDSU Dept. 7660, P.O. Box 6050, Fargo, ND 58108-6050, USA
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Abstract
Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may "pollute" the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.
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Affiliation(s)
- Duane E Falk
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G2W1, Canada.
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Balázs E, Cowling WA. Exploiting genome-wide association in oilseed Brassica species. Genome 2010; 53:853-5. [PMID: 21076500 DOI: 10.1139/g10-086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- E Balázs
- Department of Applied Genomics, H-2462 Martonvásár, Agricultural Research Institute, Brunszvik. u. 2, Hungary
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Ryan PR, Raman H, Gupta S, Sasaki T, Yamamoto Y, Delhaize E. The multiple origins of aluminium resistance in hexaploid wheat include Aegilops tauschii and more recent cis mutations to TaALMT1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:446-55. [PMID: 20804458 DOI: 10.1111/j.1365-313x.2010.04338.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Acid soils limit plant production worldwide because their high concentrations of soluble aluminium cations (Al(3+) ) inhibit root growth. Major food crops such as wheat (Triticum aestivum L.) have evolved mechanisms to resist Al(3+) toxicity, thus enabling wider distribution. The origins of Al(3+) resistance in wheat are perplexing because all progenitors of this hexaploid species are reportedly sensitive to Al(3+) stress. The large genotypic variation for Al(3+) resistance in wheat is largely controlled by expression of an anion channel, TaALMT1, which releases malate anions from the root apices. A current hypothesis proposes that the malate anions protect this sensitive growth zone by binding to Al(3+) in the apoplasm. We investigated the evolution of this trait in wheat, and demonstrated that it has multiple independent origins that enhance Al(3+) resistance by increasing TaALMT1 expression. One origin is likely to be Aegilops tauschii while other origins occurred more recently from a series of cis mutations that have generated tandemly repeated elements in the TaALMT1 promoter. We generated transgenic plants to directly compare these promoter alleles and demonstrate that the tandemly repeated elements act to enhance gene expression. This study provides an example from higher eukaryotes in which perfect tandem repeats are linked with transcriptional regulation and phenotypic change in the context of evolutionary adaptation to a major abiotic stress.
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Affiliation(s)
- Peter R Ryan
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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