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Rodríguez-Suárez C, Atienza SG. Hordeum chilense genome, a useful tool to investigate the endosperm yellow pigment content in the Triticeae. BMC PLANT BIOLOGY 2012; 12:200. [PMID: 23122232 PMCID: PMC3534404 DOI: 10.1186/1471-2229-12-200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/30/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND The wild barley Hordeum chilense fulfills some requirements for being a useful tool to investigate the endosperm yellow pigment content (YPC) in the Triticeae including its diploid constitution, the availability of genetic resources (addition and deletion stocks and a high density genetic map) and, especially, its high seed YPC not silenced in tritordeums (amphiploids derived from H. chilense and wheat). Thus, the aim of this work was to test the utility of the H. chilense genome for investigating the YPC in the Triticeae. RESULTS Twelve genes related to endosperm carotenoid content and/or YPC in grasses (Dxr, Hdr [synonym ispH], Ggpps1, Psy2, Psy3, Pds, Zds, e-Lcy, b-Lcy, Hyd3, Ccd1 and Ppo1) were identified, and mapped in H. chilense using rice genes to identify orthologs from barley, wheat, sorghum and maize. Macrocolinearity studies revealed that gene positions were in agreement in H. vulgare and H. chilense. Additionally, three main regions associated with YPC were identified in chromosomes 2Hch, 3Hch and 7Hch in H. chilense, the former being the most significant one. CONCLUSIONS The results obtained are consistent with previous findings in wheat and suggest that Ggpps1, Zds and Hyd3 on chromosome 2Hch may be considered candidate genes in wheat for further studies in YPC improvement. Considering the syntenic location of carotenoid genes in H. chilense, we have concluded that the Hch genome may constitute a valuable tool for YPC studies in the Triticeae.
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Affiliation(s)
| | - Sergio G Atienza
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo 4084, Córdoba, E-14080, Spain
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52
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Liu Y, He Z, Appels R, Xia X. Functional markers in wheat: current status and future prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1-10. [PMID: 22366867 DOI: 10.1007/s00122-012-1829-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/11/2012] [Indexed: 05/18/2023]
Abstract
Functional markers (FM) are developed from sequence polymorphisms present in allelic variants of a functional gene at a locus. FMs accurately discriminate alleles of a targeted gene, and are ideal molecular markers for marker-assisted selection in wheat breeding. In this paper, we summarize FMs developed and used in common wheat. To date, more than 30 wheat loci associated with processing quality, agronomic traits, and disease resistance, have been cloned, and 97 FMs were developed to identify 93 alleles based on the sequences of those genes. A general approach is described for isolation of wheat genes and development of FMs based on in silico cloning and comparative genomics. The divergence of DNA sequences of different alleles that affect gene function is summarized. In addition, 14 molecular markers specific for alien genes introduced from common wheat relatives were also described. This paper provides updated information on all FMs and gene-specific STS markers developed so far in wheat and should facilitate their application in wheat breeding programs.
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Affiliation(s)
- Yanan Liu
- National Wheat Improvement Centre, The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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53
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Molecular and physico-chemical evaluation of enzymatic browning of whole meal and dough in a collection of tetraploid wheats. J Cereal Sci 2012. [DOI: 10.1016/j.jcs.2012.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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54
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Beecher BS, Carter AH, See DR. Genetic mapping of new seed-expressed polyphenol oxidase genes in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1463-73. [PMID: 22311372 DOI: 10.1007/s00122-012-1801-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 01/05/2012] [Indexed: 05/22/2023]
Abstract
Polyphenol oxidase (PPO) enzymatic activity is a major cause in time-dependent discoloration in wheat dough products. The PPO-A1 and PPO-D1 genes have been shown to contribute to wheat kernel PPO activity. Recently a novel PPO gene family consisting of the PPO-A2, PPO-B2, and PPO-D2 genes has been identified and shown to be expressed in wheat kernels. In this study, the sequences of these five kernel PPO genes were determined for the spring wheat cultivars Louise and Penawawa. The two cultivars were found to be polymorphic at each of the PPO loci. Three novel alleles were isolated from Louise. The Louise X Penawawa mapping population was used to genetically map all five PPO genes. All map to the long arm of homeologous group 2 chromosomes. PPO-A2 was found to be located 8.9 cM proximal to PPO-A1 on the long arm of chromosome 2A. Similarly, PPO-D1 and PPO-D2 were separated by 10.7 cM on the long arm of chromosome 2D. PPO-B2 mapped to the long arm of chromosome 2B and was the site of a novel QTL for polyphenol oxidase activity. Five other PPO QTL were identified in this study. One QTL corresponds to the previously described PPO-D1 locus, one QTL corresponds to the PPO-D2 locus, whereas the remaining three are located on chromosome 2B.
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Affiliation(s)
- Brian S Beecher
- USDA-ARS, Wheat Genetics, Quality, Physiology and Disease Research, Pullman, WA 99164-6394, USA.
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55
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Martin JM, Berg JE, Hofer P, Kephart KD, Nash D, Bruckner PL. Allelic variation of polyphenol oxidase genes impacts on Chinese raw noodle color. J Cereal Sci 2011. [DOI: 10.1016/j.jcs.2011.08.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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56
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Beecher B, Skinner DZ. Molecular cloning and expression analysis of multiple polyphenol oxidase genes in developing wheat (Triticum aestivum) kernels. J Cereal Sci 2011. [DOI: 10.1016/j.jcs.2011.01.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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57
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HE ZH, XIA XC, CHEN XM, ZHUANG QS. Progress of Wheat Breeding in China and the Future Perspective. ZUOWU XUEBAO 2011. [DOI: 10.3724/sp.j.1006.2011.00202] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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58
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LI NY, CAI WM, JIN QL, QIN QP, RAN FL. Molecular Cloning and Expression of Polyphenoloxidase Genes from the Mushroom, Agaricus bisporus. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1671-2927(09)60305-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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59
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Sun Y, He Z, Ma W, Xia X. Alternative splicing in the coding region of Ppo-A1 directly influences the polyphenol oxidase activity in common wheat (Triticum aestivum L.). Funct Integr Genomics 2010; 11:85-93. [PMID: 21046181 DOI: 10.1007/s10142-010-0201-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 10/17/2010] [Accepted: 10/19/2010] [Indexed: 01/11/2023]
Abstract
Polyphenol oxidase (PPO) plays a crucial role in browning reactions in fresh and processed fruits and vegetables, as well as products made from cereal grains. Common wheat (Triticum aestivum L.) has a large genome, representing an interesting system to advance our understanding of plant PPO gene expression, regulation and function. In the present study, we characterized the expression of Ppo-A1, a major PPO gene located on wheat chromosome 2A, using DNA sequencing, semi-quantitative RT-PCR, PPO activity assays and whole-grain staining methods during grain development. The results indicated that the expression of the Ppo-A1b allele was regulated by alternative splicing of pre-mRNAs, resulting from a 191-bp insertion in intron 1 and one C/G SNP in exon 2. Eight mRNA isoforms were identified in developing grains based on alignments between cDNA and genomic DNA sequences. Only the constitutively spliced isoform b encodes a putative full-length PPO protein based on its coding sequence whereas the other seven spliced isoforms, a, c, d, e, f, g and h, have premature termination codons resulting in potential nonsense-mediated mRNA decay. The differences in expression of Ppo-A1a and Ppo-A1b were confirmed by PPO activity assays and whole grain staining, providing direct evidence for the influence of alternative splicing in the coding region of Ppo-A1 on polyphenol oxidase activity in common wheat grains.
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Affiliation(s)
- Youwei Sun
- Institute of Crop Science, National Wheat Improvement Centre/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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60
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Anderson JV, Fuerst EP, Tedrow T, Hulke B, Kennedy AC. Activation of polyphenol oxidase in dormant wild oat caryopses by a seed-decay isolate of Fusarium avenaceum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:10597-605. [PMID: 20853835 DOI: 10.1021/jf102625a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Incubation of dormant wild oat (Avena fatua L., isoline M73) caryopses for 1-3 days with Fusarium avenaceum seed-decay isolate F.a.1 induced activity of the plant defense enzyme polyphenol oxidase (PPO). Both extracts and leachates obtained from F.a.1-treated caryopses had decreased abundance of an ∼57 kDa antigenic PPO and increased abundance of antigenic PPOs ranging from ∼52 to 14 kDa, as compared to extracts and leachates from untreated caryopsis. Leachates from caryopsis incubated for 2 days with F.a.1 also had 5.1- and 7.5-fold more total PPO activity/g fwt and specific activity, respectively. Fractionation of leachate proteins by ion-exchange chromatography associated the majority of PPO activity with an ∼36 kDa protein from untreated caryopses and ∼36, 25, and 24 kDa proteins from F.a.1-treated caryopses. Predicted peptide sequences obtained from high-performance liquid chromatography-tandem mass spectrometry analyses indicated that the ∼57 and 36 kDa wild oat proteins had a strong similarity to wheat PPO. However, the 25 and 24 kDa proteins were most similar to a Chitinase and oxalate oxidase, respectively. Our results indicate that F.a.1-induced activation of latent PPO in wild oat caryopsis likely involves a cleavage mechanism allowing activated PPOs to be readily mobilized into their surrounding environment.
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Affiliation(s)
- James V Anderson
- Biosciences Research Laboratory, Agricultural Research Service, US Department of Agriculture, 1605 Albrecht Boulevard, Fargo, North Dakota 58102-2765, USA.
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61
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Taketa S, Matsuki K, Amano S, Saisho D, Himi E, Shitsukawa N, Yuo T, Noda K, Takeda K. Duplicate polyphenol oxidase genes on barley chromosome 2H and their functional differentiation in the phenol reaction of spikes and grains. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:3983-93. [PMID: 20616156 PMCID: PMC2935872 DOI: 10.1093/jxb/erq211] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 05/24/2010] [Accepted: 06/18/2010] [Indexed: 05/22/2023]
Abstract
Polyphenol oxidases (PPOs) are copper-containing metalloenzymes encoded in the nucleus and transported into the plastids. Reportedly, PPOs cause time-dependent discoloration (browning) of end-products of wheat and barley, which impairs their appearance quality. For this study, two barley PPO homologues were amplified using PCR with a primer pair designed in the copper binding domains of the wheat PPO genes. The full-lengths of the respective PPO genes were cloned using a BAC library, inverse-PCR, and 3'-RACE. Linkage analysis showed that the polymorphisms in PPO1 and PPO2 co-segregated with the phenol reaction phenotype of awns. Subsequent RT-PCR experiments showed that PPO1 was expressed in hulls and awns, and that PPO2 was expressed in the caryopses. Allelic variation of PPO1 and PPO2 was analysed in 51 barley accessions with the negative phenol reaction of awns. In PPO1, amino acid substitutions of five types affecting functionally important motif(s) or C-terminal region(s) were identified in 40 of the 51 accessions tested. In PPO2, only one mutant allele with a precocious stop codon resulting from an 8 bp insertion in the first exon was found in three of the 51 accessions tested. These observations demonstrate that PPO1 is the major determinant controlling the phenol reaction of awns. Comparisons of PPO1 single mutants and the PPO1PPO2 double mutant indicate that PPO2 controls the phenol reaction in the crease on the ventral side of caryopses. An insertion of a hAT-family transposon in the promoter region of PPO2 may be responsible for different expression patterns of the duplicate PPO genes in barley.
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Affiliation(s)
- Shin Taketa
- Institute of Plant Science and Resources, 2-20-1 Chuo, Okayama University, Kurashiki 710-0046, Japan.
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62
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Allelic variations of functional markers for polyphenol oxidase (PPO) genes in Indian bread wheat (Triticum aestivum L.) cultivars. J Genet 2010; 88:325-9. [PMID: 20086299 DOI: 10.1007/s12041-009-0047-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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63
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Winters A, Heywood S, Farrar K, Donnison I, Thomas A, Webb KJ. Identification of an extensive gene cluster among a family of PPOs in Trifolium pratense L. (red clover) using a large insert BAC library. BMC PLANT BIOLOGY 2009; 9:94. [PMID: 19619287 PMCID: PMC3224681 DOI: 10.1186/1471-2229-9-94] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 07/20/2009] [Indexed: 05/23/2023]
Abstract
BACKGROUND Polyphenol oxidase (PPO) activity in plants is a trait with potential economic, agricultural and environmental impact. In relation to the food industry, PPO-induced browning causes unacceptable discolouration in fruit and vegetables: from an agriculture perspective, PPO can protect plants against pathogens and environmental stress, improve ruminant growth by increasing nitrogen absorption and decreasing nitrogen loss to the environment through the animal's urine. The high PPO legume, red clover, has a significant economic and environmental role in sustaining low-input organic and conventional farms. Molecular markers for a range of important agricultural traits are being developed for red clover and improved knowledge of PPO genes and their structure will facilitate molecular breeding. RESULTS A bacterial artificial chromosome (BAC) library comprising 26,016 BAC clones with an average 135 Kb insert size, was constructed from Trifolium pratense L. (red clover), a diploid legume with a haploid genome size of 440-637 Mb. Library coverage of 6-8 genome equivalents ensured good representation of genes: the library was screened for polyphenol oxidase (PPO) genes.Two single copy PPO genes, PPO4 and PPO5, were identified to add to a family of three, previously reported, paralogous genes (PPO1-PPO3). Multiple PPO1 copies were identified and characterised revealing a subfamily comprising three variants PPO1/2, PPO1/4 and PPO1/5. Six PPO genes clustered within the genome: four separate BAC clones could be assembled onto a predicted 190-510 Kb single BAC contig. CONCLUSION A PPO gene family in red clover resides as a cluster of at least 6 genes. Three of these genes have high homology, suggesting a more recent evolutionary event. This PPO cluster covers a longer region of the genome than clusters detected in rice or previously reported in tomato. Full-length coding sequences from PPO4, PPO5, PPO1/5 and PPO1/4 will facilitate functional studies and provide genetic markers for plant breeding.
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Affiliation(s)
- Ana Winters
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Sue Heywood
- CNAP Artemisia Research Project, Department of Biology – Area 7, University of York, Heslington, PO Box 373, York, YO10 5YW, UK
| | - Kerrie Farrar
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Iain Donnison
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Ann Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - K Judith Webb
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
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64
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ZHAO JL, CHEN MS, MA YM, LI RJ, REN YP, SUN QQ, LI SS. QTL Mapping for Quality Traits of Chinese Dry Noodle. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(08)60224-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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65
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Wang LH, Zhao XL, He ZH, Ma W, Appels R, Peña RJ, Xia XC. Characterization of low-molecular-weight glutenin subunit Glu-B3 genes and development of STS markers in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:525-39. [PMID: 18989655 DOI: 10.1007/s00122-008-0918-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Accepted: 10/14/2008] [Indexed: 05/22/2023]
Abstract
Low-molecular-weight glutenin subunit (LMW-GS) Glu-B3 has a significant influence on the processing quality of the end-use products of common wheat. To characterize the LMW-GS genes at the Glu-B3 locus, gene-specific PCR primers were designed to amplify eight near-isogenic lines and Cheyenne with different Glu-B3 alleles (a, b, c, d, e, f, g, h and i) defined by protein electrophoretic mobility. The complete coding regions of four Glu-B3 genes with complete coding sequence were obtained and designated as GluB3-1, GluB3-2, GluB3-3 and GluB3-4. Ten allele-specific PCR markers designed from the SNPs present in the sequenced variants discriminated the Glu-B3 proteins of electrophoretic mobility alleles a, b, c, d, e, f, g, h and i. These markers were validated on 161 wheat varieties and advanced lines with different Glu-B3 alleles, thus confirming that the markers can be used in marker-assisted breeding for wheat grain processing quality.
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Affiliation(s)
- L H Wang
- Institute of Crop Science, National Wheat Improvement Centre/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
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66
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Fuerst EP, Xu SS, Beecher B. Genetic characterization of kernel polyphenol oxidases in wheat and related species. J Cereal Sci 2008. [DOI: 10.1016/j.jcs.2007.10.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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67
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He XY, Zhang YL, He ZH, Wu YP, Xiao YG, Ma CX, Xia XC. Characterization of phytoene synthase 1 gene (Psy1) located on common wheat chromosome 7A and development of a functional marker. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:213-21. [PMID: 17943267 DOI: 10.1007/s00122-007-0660-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 09/27/2007] [Indexed: 05/08/2023]
Abstract
Phytoene synthase (Psy), a critical enzyme in the carotenoid biosynthetic pathway, demonstrated high association with the yellow pigment (YP) content in wheat grain. Characterization of Psy genes and the development of functional markers for them are of importance for marker-assisted selection in wheat breeding. In this study, the full-length genomic DNA sequence of a Psy gene (Psy-A1) located on chromosome 7A, was characterized by in silico cloning and experimental validation. The cloned Psy-A1 comprises six exons and five introns, 4,175 bp in total, and an ORF of 1,284 bp. A co-dominant marker, YP7A, was developed based on polymorphisms of two haplotypes of Psy-A1, yielding 194 and 231-bp fragments in cultivars with high and low YP content, respectively. The marker YP7A was mapped on chromosome 7AL using an RIL population from cross PH82-2/Neixing 188, and a set of Chinese Spring nullisomic-tetrasomic lines and ditelosomic line 7AS. Psy-A1, co-segregating with the STS marker YP7A, was linked to SSR marker Xwmc809 on chromosome 7AL with a genetic distance of 5.8 cM, and explained 20-28% of the phenotypic variance for YP content across three environments. A total of 217 Chinese wheat cultivars and advanced lines were used to validate the association between the polymorphic band pattern and grain YP content. The results showed that the functional marker YP7A was closely related to grain YP content and, therefore, could be used in wheat breeding programs targeting of YP content for various wheat-based products.
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Affiliation(s)
- X Y He
- Institute of Crop Science, National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Zhongguancun South Street 12, Beijing 100081, China
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