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Tamisier L, Szadkowski M, Nemouchi G, Lefebvre V, Szadkowski E, Duboscq R, Santoni S, Sarah G, Sauvage C, Palloix A, Moury B. Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding. MOLECULAR PLANT PATHOLOGY 2020; 21:3-16. [PMID: 31605444 PMCID: PMC6913244 DOI: 10.1111/mpp.12874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
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Affiliation(s)
- Lucie Tamisier
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
- Present address:
Plant Pathology LaboratoryTERRA‐Gembloux Agro‐Bio TechUniversity of LiègePassage des Déportés, 25030GemblouxBelgium
| | - Marion Szadkowski
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
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Barbary A, Djian-Caporalino C, Marteu N, Fazari A, Caromel B, Castagnone-Sereno P, Palloix A. Plant Genetic Background Increasing the Efficiency and Durability of Major Resistance Genes to Root-knot Nematodes Can Be Resolved into a Few Resistance QTLs. FRONTIERS IN PLANT SCIENCE 2016; 7:632. [PMID: 27242835 PMCID: PMC4861812 DOI: 10.3389/fpls.2016.00632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/25/2016] [Indexed: 05/24/2023]
Abstract
With the banning of most chemical nematicides, the control of root-knot nematodes (RKNs) in vegetable crops is now based essentially on the deployment of single, major resistance genes (R-genes). However, these genes are rare and their efficacy is threatened by the capacity of RKNs to adapt. In pepper, several dominant R-genes are effective against RKNs, and their efficacy and durability have been shown to be greater in a partially resistant genetic background. However, the genetic determinants of this partial resistance were unknown. Here, a quantitative trait loci (QTL) analysis was performed on the F2:3 population from the cross between Yolo Wonder, an accession considered partially resistant or resistant, depending on the RKN species, and Doux Long des Landes, a susceptible cultivar. A genetic linkage map was constructed from 130 F2 individuals, and the 130 F3 families were tested for resistance to the three main RKN species, Meloidogyne incognita, M. arenaria, and M. javanica. For the first time in the pepper-RKN pathosystem, four major QTLs were identified and mapped to two clusters. The cluster on chromosome P1 includes three tightly linked QTLs with specific effects against individual RKN species. The fourth QTL, providing specific resistance to M. javanica, mapped to pepper chromosome P9, which is known to carry multiple NBS-LRR repeats, together with major R-genes for resistance to nematodes and other pathogens. The newly discovered cluster on chromosome P1 has a broad spectrum of action with major additive effects on resistance. These data highlight the role of host QTLs involved in plant-RKN interactions and provide innovative potential for the breeding of new pepper cultivars or rootstocks combining quantitative resistance and major R-genes, to increase both the efficacy and durability of RKN control by resistance genes.
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Affiliation(s)
- Arnaud Barbary
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Caroline Djian-Caporalino
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Nathalie Marteu
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Ariane Fazari
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Bernard Caromel
- INRA, UR1052, Génétique et Amélioration des Fruits et LégumesMontfavet, France
| | - Philippe Castagnone-Sereno
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Alain Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et LégumesMontfavet, France
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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra DL, Luo X, Cui J, Rivera-Bustamante RF, Li S, Hu K. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep 2016; 6:18919. [PMID: 26739748 PMCID: PMC4703971 DOI: 10.1038/srep18919] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 02/05/2023] Open
Abstract
The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Diana L. Trejo-Saavedra
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Xirong Luo
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Rafael F. Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Huang LK, Yan HD, Zhao XX, Zhang XQ, Wang J, Frazier T, Yin G, Huang X, Yan DF, Zang WJ, Ma X, Peng Y, Yan YH, Liu W. Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerataL.) through transcriptome analysis. Mol Ecol Resour 2015; 15:1497-509. [DOI: 10.1111/1755-0998.12418] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/08/2015] [Accepted: 04/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- L. K. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - H. D. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. X. Zhao
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Q. Zhang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - J. Wang
- Agronomy Department; University of Florida; Gainesville FL 32611 USA
| | - T. Frazier
- Department of Horticulture; Virginia Tech; Blacksburg VA 24061 USA
| | - G. Yin
- Department of Crop, Soil, and Environmental Sciences; University of Arkansas; Fayetteville AR 72704 USA
| | - X. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - D. F. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. J. Zang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Ma
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. Peng
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. H. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. Liu
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
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Yang H, Li C, Lam HM, Clements J, Yan G, Zhao S. Sequencing consolidates molecular markers with plant breeding practice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:779-95. [PMID: 25821196 DOI: 10.1007/s00122-015-2499-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/14/2015] [Indexed: 05/20/2023]
Abstract
Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding. The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.
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Affiliation(s)
- Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia,
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Yang M, Xu L, Liu Y, Yang P. RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera). PLoS One 2015; 10:e0125702. [PMID: 25928215 PMCID: PMC4416007 DOI: 10.1371/journal.pone.0125702] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/21/2015] [Indexed: 01/11/2023] Open
Abstract
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5’ first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus.
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Affiliation(s)
- Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Liming Xu
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail:
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8
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Quenouille J, Paulhiac E, Moury B, Palloix A. Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants. Heredity (Edinb) 2014; 112:579-87. [PMID: 24569635 DOI: 10.1038/hdy.2013.138] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/06/2013] [Accepted: 11/08/2013] [Indexed: 11/09/2022] Open
Abstract
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr2(3) and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h(2)=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr2(3) breakdown frequency. Three of the four QTLs controlling pvr2(3) breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr2(3) and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long-term farmer selection.
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Affiliation(s)
- J Quenouille
- 1] INRA, UR1052 GAFL, Montfavet Cedex, France [2] INRA, UR407 Pathologie Végétale, Montfavet Cedex, France
| | - E Paulhiac
- INRA, UR1052 GAFL, Montfavet Cedex, France
| | - B Moury
- INRA, UR407 Pathologie Végétale, Montfavet Cedex, France
| | - A Palloix
- INRA, UR1052 GAFL, Montfavet Cedex, France
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9
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Li MY, Wang F, Jiang Q, Ma J, Xiong AS. Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing. HORTICULTURE RESEARCH 2014; 1:10. [PMID: 26504532 PMCID: PMC4596314 DOI: 10.1038/hortres.2014.10] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/18/2014] [Accepted: 01/17/2014] [Indexed: 05/18/2023]
Abstract
Celery (Apium graveolens L.) is one of the most important and widely grown vegetables in the Apiaceae family. Due to the lack of comprehensive genomic resources, research on celery has mainly utilized physiological and biochemical approaches, rather than molecular biology, to study this crop. Transcriptome sequencing has become an efficient and economic technology for obtaining information on gene expression that can greatly facilitate molecular and genomic studies of species for which a sequenced genome is not available. In the present study, 15 893 516 and 19 818 161 high-quality sequences were obtained by RNA-seq from two celery varieties 'Ventura' and 'Jinnan Shiqin', respectively. The obtained reads were assembled into 39 584 and 41 740 unigenes with mean lengths of 683 bp and 690 bp, respectively. A total of 1939 simple sequence repeat (SSR) markers were identified in 'Ventura' and 2004 SSRs in 'Jinnan Shiqin'. Di-nucleotide repeats were the most common repeat motif, accounting for 55.49% and 54.84% in 'Ventura' and 'Jinnan Shiqin', respectively. A comparison of expressed genes between the two libraries, identified 338 differentially expressed genes (DEGs). Three hundred and three of the DEGs were annotated based on a sequence similarity search utilizing eight public databases. Additionally, the expression profile of eight annotated DEGs was characterized in response to abiotic stresses. The collective data generated in the present research represent a valuable resource for further genetic and molecular studies in celery.
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Affiliation(s)
- Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China of Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China of Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China of Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China of Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China of Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- ()
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10
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Alimi NA, Bink MCAM, Dieleman JA, Magán JJ, Wubs AM, Palloix A, van Eeuwijk FA. Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2597-625. [PMID: 23903631 DOI: 10.1007/s00122-013-2160-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/12/2013] [Indexed: 05/24/2023]
Abstract
A mixed model framework was defined for QTL analysis of multiple traits across multiple environments for a RIL population in pepper. Detection power for QTLs increased considerably and detailed study of QTL by environment interactions and pleiotropy was facilitated. For many agronomic crops, yield is measured simultaneously with other traits across multiple environments. The study of yield can benefit from joint analysis with other traits and relations between yield and other traits can be exploited to develop indirect selection strategies. We compare the performance of three multi-response QTL approaches based on mixed models: a multi-trait approach (MT), a multi-environment approach (ME), and a multi-trait multi-environment approach (MTME). The data come from a multi-environment experiment in pepper, for which 15 traits were measured in four environments. The approaches were compared in terms of number of QTLs detected for each trait, the explained variance, and the accuracy of prediction for the final QTL model. For the four environments together, the superior MTME approach delivered a total of 47 regions containing putative QTLs. Many of these QTLs were pleiotropic and showed quantitative QTL by environment interaction. MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. The large number of model parameters in the MTME approach was challenging and we propose several guidelines to help obtain a stable final QTL model. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.
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Affiliation(s)
- N A Alimi
- Biometris-Wageningen University & Research Centre, P. O. Box 100, 6700 AC, Wageningen, The Netherlands
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11
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Gao C, Ren X, Mason AS, Li J, Wang W, Xiao M, Fu D. Revisiting an important component of plant genomes: microsatellites. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:645-661. [PMID: 32481138 DOI: 10.1071/fp12325] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/16/2013] [Indexed: 06/11/2023]
Abstract
Microsatellites are some of the most highly variable repetitive DNA tracts in genomes. Few studies focus on whether the characteristic instability of microsatellites is linked to phenotypic effects in plants. We summarise recent data to investigate how microsatellite variations affect gene expression and hence phenotype. We discuss how the basic characteristics of microsatellites may contribute to phenotypic effects. In summary, microsatellites in plants are universal and highly mutable, they coexist and coevolve with transposable elements, and are under selective pressure. The number of motif nucleotides, the type of motif and transposon activity all contribute to the nonrandom generation and decay of microsatellites, and to conservation and distribution biases. Although microsatellites are generated by accident, they mature through responses to environmental change before final decay. This process is mediated by organism adjustment mechanisms, which maintain a balance between birth versus death and growth versus decay in microsatellites. Close relationships also exist between the physical structure, variation and functionality of microsatellites: in most plant species, sequences containing microsatellites are associated with catalytic activity and binding functions, are expressed in the membrane and organelles, and participate in the developmental and metabolic processes. Microsatellites contribute to genome structure and functional plasticity, and may be considered to promote species evolution in plants in response to environmental changes. In conclusion, the generation, loss, functionality and evolution of microsatellites can be related to plant gene expression and functional alterations. The effect of microsatellites on phenotypic variation may be as significant in plants as it is in animals.
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Affiliation(s)
- Caihua Gao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaodong Ren
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Annaliese S Mason
- Centre for Integrative Legume Research and School of Agriculture and Food Sciences, The University of Queensland, Brisbane 4072, Qld, Australia
| | - Jiana Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wei Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Meili Xiao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
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Liu C, Ma N, Wang PY, Fu N, Shen HL. Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper (Capsicum annuum L.). PLoS One 2013; 8:e65209. [PMID: 23750245 PMCID: PMC3672106 DOI: 10.1371/journal.pone.0065209] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 04/23/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility. RESULTS We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen. CONCLUSIONS Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.
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Affiliation(s)
- Chen Liu
- China Agricultural University, Beijing, China
| | - Ning Ma
- China Agricultural University, Beijing, China
| | | | - Nan Fu
- China Agricultural University, Beijing, China
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Góngora-Castillo E, Buell CR. Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Nat Prod Rep 2013; 30:490-500. [PMID: 23377493 DOI: 10.1039/c3np20099j] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Plant natural product research can be facilitated through genome and transcriptome sequencing approaches that generate informative sequence and expression datasets that enable characterization of biochemical pathways of interest. As the overwhelming majority of plant-derived natural products are derived from species with little, if any, sequence and/or genomic resources, the ability to perform whole genome shotgun sequencing and assembly has been and will continue to be transformative as access to a genome sequence provides molecular resources and a context for discovery and characterization of biosynthetic pathways. Due to the reduced size and complexity of the transcriptome relative to the genome, transcriptome sequencing provides a rapid, inexpensive approach to access gene sequences, gene expression abundances, and gene expression patterns in any species, including those that lack a reference genome sequence. To date, successful applications of RNA sequencing in conjunction with de novo transcriptome assembly has enabled identification of new genes in an array of biochemical pathways in plants. While sequencing technologies are well developed, challenges remain in the handling and analysis of transcriptome sequences. In this Highlight article, we provide an overview of the bioinformatics challenges associated with transcriptome analyses using short read sequences and how to address these issues in plant species that lack a reference genome.
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He L, Xu X, Li Y, Li C, Zhu Y, Yan H, Sun Z, Sun C, Song J, Bi Y, Shen J, Cheng R, Wang Z, Xiao W, Chen S. Transcriptome analysis of buds and leaves using 454 pyrosequencing to discover genes associated with the biosynthesis of active ingredients in Lonicera japonica Thunb. PLoS One 2013; 8:e62922. [PMID: 23638167 PMCID: PMC3636143 DOI: 10.1371/journal.pone.0062922] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 03/29/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are relatively well known, the genetic information available for this species, especially the biosynthetic pathways of its active ingredients, is limited. METHODOLOGY/PRINCIPAL FINDINGS We obtained one million reads (average length of 400 bp) in a whole sequence run using a Roche/454 GS FLX titanium platform. Altogether, 85.69% of the unigenes covering the entire life cycle of the plant were annotated and 325 unigenes were assigned to secondary metabolic pathways. Moreover, 2039 unigenes were predicted as transcription factors. Nearly all of the possible enzymes involved in the biosynthesis of CGA and luteoloside were discovered in L. japonica. Three hydroxycinnamoyl transferase genes, including two hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase genes and one hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) gene featuring high similarity to known genes from other species, were cloned. The HCT gene was discovered for the first time in L. japonica. In addition, 188 candidate cytochrome P450 unigenes and 245 glycosyltransferase unigenes were found in the expressed sequence tag (EST) dataset. CONCLUSION This study provides a high quality EST database for L. japonica by 454 pyrosequencing. Based on the EST annotation, a set of putative genes involved in CGA and luteoloside biosynthetic pathways were discovered. The database serves as an important source of public information on genetic markers, gene expression, genomics, and functional genomics in L. japonica.
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Affiliation(s)
- Liu He
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolan Xu
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Li
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunfang Li
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingjie Zhu
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haixia Yan
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiying Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu’an Bi
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process; Jiangsu Kanion Pharmaceutical Co. LTD, Lianyungang, China
| | - Juan Shen
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process; Jiangsu Kanion Pharmaceutical Co. LTD, Lianyungang, China
| | - Ruiyang Cheng
- Beijing University of Chinese Medicine, Beijing, China
| | - Zhenzhong Wang
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process; Jiangsu Kanion Pharmaceutical Co. LTD, Lianyungang, China
| | - Wei Xiao
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process; Jiangsu Kanion Pharmaceutical Co. LTD, Lianyungang, China
| | - Shilin Chen
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
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Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). APPLICATIONS IN PLANT SCIENCES 2013; 1:apps.1200011. [PMID: 25202520 PMCID: PMC4105277 DOI: 10.3732/apps.1200011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 05/03/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. • METHODS AND RESULTS More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. • CONCLUSIONS To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.
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Affiliation(s)
- Samuel E. Fox
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Justin Preece
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jeffrey A. Kimbrel
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608 USA
| | - Gina L. Marchini
- Department of Biology, Portland State University, Portland, Oregon 97201 USA
| | - Abigail Sage
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 USA
| | - Mitchell B. Cruzan
- Department of Biology, Portland State University, Portland, Oregon 97201 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
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