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Zhang Y, Shi J, Shen C, To VT, Shi Q, Ye L, Shi J, Zhang D, Chen W. Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars. PLANT CELL REPORTS 2022; 41:2279-2292. [PMID: 36209436 DOI: 10.1007/s00299-022-02920-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars. Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deletions) have become popular because of their abundance and ease of detection, discovery of genome-wide DNA polymorphisms and development of InDel markers in barley have lagged behind other cereal crops such as rice, maize and wheat. In this study, we re-sequenced two barley cultivars, Golden Promise (GP, a classic British spring barley variety) and Hua30 (a Chinese spring barley variety), and mapped clean reads to the reference Morex genome, and identified in total 13,933,145 single nucleotide polymorphisms (SNPs) and 1,240,456 InDels for GP with Morex, 11,297,100 SNPs and 781,687 InDels for Hua30 with Morex, and 13,742,399 SNPs and 1,191,597 InDels for GP with Hua30. We further characterized distinct types, chromosomal distribution patterns, genome location, functional effect, and other features of these DNA polymorphisms. Additionally, we revealed the functional relevance of these identified SNPs/InDels regarding different flowering times between Hua30 and GP within 17 flowering time genes. Furthermore, we developed a series of InDel markers and validated them experimentally in 43 barley core accessions, respectively. Finally, we rebuilt population structure and phylogenetic tree of these 43 barley core accessions. Collectively, all of these genetic resources will facilitate not only the basic research but also applied research in barley.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Vinh-Trieu To
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingzhen Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia, 5064, Australia.
| | - Weiwei Chen
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia, 5064, Australia.
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Genetic diversity, population structure and relationship of Ethiopian barley (Hordeum vulgare L.) landraces as revealed by SSR markers. J Genet 2022. [DOI: 10.1007/s12041-021-01346-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Ge C, Wentzel E, D'Souza N, Chen K, Oliver RP, Ellwood SR. Adult resistance genes to barley powdery mildew confer basal penetration resistance associated with broad-spectrum resistance. THE PLANT GENOME 2021; 14:e20129. [PMID: 34392613 DOI: 10.1002/tpg2.20129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew isa major disease of barley (Hordeum vulgare L.) for which breeders have traditionally relied on dominant, pathogen race-specific resistance genes for genetic control. Directional selection pressures in extensive monocultures invariably result in such genes being overcome as the pathogen mutates to evade recognition. This has led to a widespread reliance on fungicides and a single broad-spectrum recessive resistance provided by the mlo gene. The range of resistance genes and alleles found in wild crop relatives and landraces has been reduced in agricultural cultivars through an erosion of genetic diversity during domestication and selective breeding. Three novel major-effect adult plant resistance (APR) genes from landraces, designated Resistance to Blumeria graminis f. sp. hordei (Rbgh1 to Rbgh3), were identified in the terminal regions of barley chromosomes 5HL, 7HS, and 1HS, respectively. The phenotype of the new APR genes showed neither pronounced penetration resistance, nor the spontaneous necrosis and mesophyll cell death typical of mlo resistance, nor a whole epidermal cell hypersensitive response, typical of race-specific resistance. Instead, resistance was localized to the site of attempted penetration in an epidermal cell and was associated with cell wall appositions and cytosolic vesicle-like bodies, and lacked strong induction of reactive oxygen species. The APR genes exhibited differences in vesicle-like body sizes, their distribution, and the extent of localized 3,3-diaminobenzidine staining in individual doubled haploid lines. The results revealed a set of unique basal penetration resistance genes that offer opportunities for combining different resistance mechanisms in breeding programs for robust mildew resistance.
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Affiliation(s)
- Cynthia Ge
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Elzette Wentzel
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Nola D'Souza
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Kefei Chen
- Statistics for the Australian Grains Industry-West, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Richard P Oliver
- School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin Univ., Bentley, WA, 6102, Australia
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QTL Mapping and Phenotypic Variation for Seedling Vigour Traits in Barley ( Hordeum vulgare L.). PLANTS 2021; 10:plants10061149. [PMID: 34200109 PMCID: PMC8227620 DOI: 10.3390/plants10061149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022]
Abstract
Seed vigour is considered a critical stage for barley production, and cultivars with early seedling vigour (ESV) facilitate rapid canopy formation. In this study, QTLs for 12 ESV-related traits were mapped using 185 RILs derived from a Xena x H94061120 evaluated across six independent environments. DArT markers were used to develop a genetic map (1075.1 cM; centimorgans) with an average adjacent-marker distance of 3.28 cM. In total, 46 significant QTLs for ESV-related traits were detected. Fourteen QTLs for biomass yield were found on all chromosomes, two of them co-localized with QTLs on 1H for grain yield. The related traits: length of the first and second leaves and dry weight of the second leaf, biomass yield and grain yield, had high heritability (>30%). Meanwhile, a significant correlation was observed between grain yield and biomass yield, which provided a clear image of these traits in the selection process. Our results demonstrate that a pleiotropic QTL related to the specific leaf area of the second leaf, biomass yield, and grain yield was linked to the DArT markers bPb-9280 and bPb-9108 on 1H, which could be used to significantly improve seed vigour by marker-assisted selection and facilitate future map-based cloning efforts.
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Wang W, He J, Chen S, Peng P, Zhong W, Wang X, Zhang T, Li Y. Construction of a high-density genetic map and fine mapping of a candidate gene locus for a novel branched-spike mutant in barley. PLoS One 2020; 15:e0227617. [PMID: 31914168 PMCID: PMC6948822 DOI: 10.1371/journal.pone.0227617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/24/2019] [Indexed: 11/19/2022] Open
Abstract
A Yunnan branched-spike (Ynbs) barley mutant is useful for study of the genetic mechanisms underlying variation in barley spike architecture. In the current study, a mutant (Ynbs-1), a recombinant inbred line (RIL-1), and a cultivar (BDM-8) were used as parents to develop populations. Ynbs-1 exhibits typical branched spike, whereas the others exhibit six-row spike. Genetic analysis on their F1, F2 and F3 populations showed that one recessive gene is responsible for the branched spike trait. SLAF marker generated from specific locus amplified fragment sequencing (SLAF-seq) was used to genotype the populations. A high-density genetic map of barley was constructed using 14,348 SLAF markers, which covered all 7 chromosomes at 1,347.44 cM in length with an average marker density of 0.09 cM between adjacent markers. Linkage analysis of the branched-spike trait using the genetic map indicated that branched spike trait in the Ynbs-1 is controlled by single locus on chromosome 2H at the interval between 65.00 and 65.47 cM that is flanked by Marker310119 and Marker2679451. Several candidate genes that may be responsible for barley multiple-spikelet degeneration, single-floret spikelet increase and seed set rate decrease were identified in the region. The high-density genetic map and the gene locus revealed in this study provide valuable information for elucidating the genetic mechanism of spike branching in barley.
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Affiliation(s)
- Weibin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Junyu He
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shengwei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- * E-mail:
| | - Peng Peng
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei Zhong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xintian Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Tingting Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuping Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
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Fang Y, Zhang X, Zhang X, Tong T, Zhang Z, Wu G, Hou L, Zheng J, Niu C, Li J, Wang W, Wang H, Xue D. A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2020; 11:620922. [PMID: 33424912 PMCID: PMC7793689 DOI: 10.3389/fpls.2020.620922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/26/2020] [Indexed: 05/12/2023]
Abstract
Grain size is an important agronomic trait determines yield in barley, and a high-density genetic map is helpful to accurately detect quantitative trait loci (QTLs) related to grain traits. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, a high-density genetic map was constructed with a population of 134 recombinant inbred lines (RILs) deriving from a cross between Golden Promise (GP) and H602, which contained 12,635 SLAFs with 26,693 SNPs, and spanned 896.74 cM with an average interval of 0.07 cM on seven chromosomes. Based on the map, a total of 16 QTLs for grain length (GL), grain width and thousand-grain weight were detected on 1H, 2H, 4H, 5H, and 6H. Among them, a major QTL locus qGL1, accounting for the max phenotypic variance of 16.7% was located on 1H, which is a new unreported QTL affecting GL. In addition, the other two QTLs, qGL5 and qTGW5, accounting for the max phenotypic variances of 20.7 and 21.1%, respectively, were identified in the same region, and sequencing results showed they are identical to HvDep1 gene. These results indicate that it is a feasible approach to construct a high-quality genetic map for QTL mapping by using SLAF markers, and the detected major QTLs qGL1, qGL5, and qTGW5 are useful for marker-assisted selection (MAS) of grain size in barley breeding.
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Affiliation(s)
- Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xian Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ziling Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Gengwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Linlin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Junjun Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chunyu Niu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jia Li
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Wenjia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Hua Wang,
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Dawei Xue,
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Saito M, Tanaka T, Sato K, Vrinten P, Nakamura T. A single nucleotide polymorphism in the "Fra" gene results in fractured starch granules in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:353-364. [PMID: 29098311 DOI: 10.1007/s00122-017-3006-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 10/26/2017] [Indexed: 05/23/2023]
Abstract
We report here that the mutation causing fractured starch granules in the barley line "Franubet" results from a point mutation in the barley gene corresponding to the rice FLO6 gene. The "fra" mutation in barley, which was originally isolated and characterized over 30 years ago, results in fractured starch granules and an opaque phenotype. This mutation has been used in breeding programs, since it appears to be useful in the production of pearled barley for human consumption. However, selection for this phenotype is difficult, since wild-type and heterozygous kernels cannot be distinguished phenotypically, and until now, the gene involved in this mutation has not been determined. Here, we used a map-based cloning approach using nanopore sequencing to obtain long reads from a BAC clone carrying markers on either side of the fra locus. By fine mapping followed by aligning RNA-seq reads to four genes within the mapped region, we were able to determine that the fra mutation is caused by the introduction of a stop codon in the barley homologue of the rice FLOURY ENDOSPERM 6 (FLO6) gene. This gene has a CBM48 domain that binds to starch, and may act through interactions with isoamylase1 (ISA1), assisting in the binding of ISA1 to starch granules. Perfect markers able to distinguish all genotypes were designed and tested in several large populations; in all cases, the markers were able to distinguish wild-type, heterozygous, and mutant genotypes.
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Affiliation(s)
- Mika Saito
- NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan
| | | | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Patricia Vrinten
- Bioriginal Food and Science Corporation, Saskatoon, S7J 0R1, Canada
| | - Toshiki Nakamura
- NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
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9
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Zhang XW, Jiang QT, Wei YM, Liu C. Inheritance analysis and mapping of quantitative trait loci (QTL) controlling individual anthocyanin compounds in purple barley (Hordeum vulgare L.) grains. PLoS One 2017; 12:e0183704. [PMID: 28832657 PMCID: PMC5568277 DOI: 10.1371/journal.pone.0183704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 11/19/2022] Open
Abstract
Anthocyanin-rich barley can have great potential in promoting human health and in developing nutraceuticals and functional foods. As different anthocyanin compounds have different antioxidant activities, breeding cultivars with pre-designed anthocyanin compositions could be highly desirable. Working toward this possibility, we assessed and reported for the first time the genetic control of individual anthocyanin compounds in barley. Of the ten anthocyanins assessed, two, peonidin-3-glucoside (P3G) and cyanidin-3-glucoside (C3G), were major components in the purple pericarp barley genotype RUSSIA68. Quantitative trait locus (QTL) mapping showed that both anthocyanin compounds were the interactive products of two loci, one located on chromosome arm 2HL and the other on 7HS. However, the two different anthocyanin components seem to be controlled by different interactions between the two loci. The effects of the 7HS locus on P3G and C3G were difficult to detect without removing the effect of the 2HL locus. At least one copy of the 2HL alleles from the purple pericarp parent was required for the synthesis of P3G. This does not seem to be the case for the production of C3G which was produced in each of all the different allele combinations between the two loci. Typical maternal effect was also observed in the inheritance of purple pericarp grains in barley. The varied values of different compounds, coupled with their different genetic controls, highlight the need for targeting individual anthocyanins in crop breeding and food processing.
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Affiliation(s)
- Xiao-Wei Zhang
- CSIRO Agriculture & Food, St Lucia, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Chunji Liu
- CSIRO Agriculture & Food, St Lucia, Queensland, Australia
- * E-mail:
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SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley. Sci Rep 2016; 6:31741. [PMID: 27530597 PMCID: PMC4987670 DOI: 10.1038/srep31741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/26/2016] [Indexed: 11/08/2022] Open
Abstract
A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.
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Wang J, Sun G, Ren X, Li C, Liu L, Wang Q, Du B, Sun D. QTL underlying some agronomic traits in barley detected by SNP markers. BMC Genet 2016; 17:103. [PMID: 27388211 PMCID: PMC4936321 DOI: 10.1186/s12863-016-0409-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/24/2016] [Indexed: 12/30/2022] Open
Abstract
Background Increasing the yield of barley (Hordeum vulgare L.) is a main breeding goal in developing barley cultivars. A high density genetic linkage map containing 1894 SNP and 68 SSR markers covering 1375.8 cM was constructed and used for mapping quantitative traits. A late-generation double haploid population (DH) derived from the Huaai 11 × Huadamai 6 cross was used to identify QTLs and QTL × environment interactions for ten traits affecting grain yield including length of main spike (MSL), spikelet number on main spike (SMS), spikelet number per plant (SLP), grain number per plant (GP), grain weight per plant (GWP), grain number per spike (GS), thousand grain weight (TGW), grain weight per spike (GWS), spike density (SPD) and spike number per plant (SP). Results In single environment analysis using composite interval mapping (CIM), a total of 221 QTLs underlying the ten traits were detected in five consecutive years (2009–2013). The QTLs detected in each year were 50, 48, 41, 41 and 41 for the year 2009 to 2013. The QTLs associated with these traits were generally clustered on chromosome 2H, 4H and 7H. In multi-environment analysis, a total of 111 significant QTLs including 18 for MSL, 16 for SMS, 15 for SPD, 5 for SP, 4 for SLP, 14 for TGW, 5 for GP, 11 for GS, 8 for GWP, and 15 for GWS were detected in the five years. Most QTLs showed significant QTL × environment interactions (QEI), nine QTLs (qIMSL3-1, qIMSL4-1, qIMSL4-2, qIMSL6-1, qISMS7-1, qISPD2-7, qISPD7-1, qITGW3-1 and qIGWS4-3) were detected with minimal QEI effects and stable in different years. Among 111 QTLs,71 (63.40 %) QTLs were detected in both single and multiple environments. Conclusions Three main QTL cluster regions associated with the 10 agronomic traits on chromosome 2H, 4H and 7H were detected. The QTLs for SMS, SLP, GP and GWP were located in the region near Vrs1 on chromosome 2H. The QTLs underlying SMS, SPD and SLP were clustered on chromosome 4H. On the terminal of chromosome 7H, there was a QTL cluster associated with TGW, SPD, GWP and GWS. The information will be useful for marker-assisted selection (MAS) in barley breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0409-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, 923 Robie Street, Halifax, NS, B3H 3C3, Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chengdao Li
- Department of Agriculture & Food/Agricultural Research Western Australia, 3 Baron-Hay Court, South Perth, WA, 6155, Australia
| | - Lipan Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, 434025, Hubei, China.
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Mikołajczak K, Ogrodowicz P, Gudyś K, Krystkowiak K, Sawikowska A, Frohmberg W, Górny A, Kędziora A, Jankowiak J, Józefczyk D, Karg G, Andrusiak J, Krajewski P, Szarejko I, Surma M, Adamski T, Guzy-Wróbelska J, Kuczyńska A. Quantitative Trait Loci for Yield and Yield-Related Traits in Spring Barley Populations Derived from Crosses between European and Syrian Cultivars. PLoS One 2016; 11:e0155938. [PMID: 27227880 PMCID: PMC4881963 DOI: 10.1371/journal.pone.0155938] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/08/2016] [Indexed: 11/18/2022] Open
Abstract
In response to climatic changes, breeding programmes should be aimed at creating new cultivars with improved resistance to water scarcity. The objective of this study was to examine the yield potential of barley recombinant inbred lines (RILs) derived from three cross-combinations of European and Syrian spring cultivars, and to identify quantitative trait loci (QTLs) for yield-related traits in these populations. RILs were evaluated in field experiments over a period of three years (2011 to 2013) and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers; a genetic map for each population was constructed and then one consensus map was developed. Biological interpretation of identified QTLs was achieved by reference to Ensembl Plants barley gene space. Twelve regions in the genomes of studied RILs were distinguished after QTL analysis. Most of the QTLs were identified on the 2H chromosome, which was the hotspot region in all three populations. Syrian parental cultivars contributed alleles decreasing traits' values at majority of QTLs for grain weight, grain number, spike length and time to heading, and numerous alleles increasing stem length. The phenomic and molecular approaches distinguished the lines with an acceptable grain yield potential combining desirable features or alleles from their parents, that is, early heading from the Syrian breeding line (Cam/B1/CI08887//CI05761) and short plant stature from the European semidwarf cultivar (Maresi).
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Affiliation(s)
- Krzysztof Mikołajczak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Kornelia Gudyś
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40–032 Katowice, Poland
| | - Karolina Krystkowiak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Aneta Sawikowska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Wojciech Frohmberg
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Andrzej Górny
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Andrzej Kędziora
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Janusz Jankowiak
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Damian Józefczyk
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Grzegorz Karg
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Joanna Andrusiak
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40–032 Katowice, Poland
| | - Maria Surma
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Tadeusz Adamski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Justyna Guzy-Wróbelska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40–032 Katowice, Poland
- * E-mail: (AK); (JGW)
| | - Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
- * E-mail: (AK); (JGW)
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Hua W, Zhang XQ, Zhu J, Shang Y, Wang J, Jia Q, Zhang Q, Yang J, Li C. Identification and Fine Mapping of a White Husk Gene in Barley (Hordeum vulgare L.). PLoS One 2016; 11:e0152128. [PMID: 27028408 PMCID: PMC4814061 DOI: 10.1371/journal.pone.0152128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/09/2016] [Indexed: 11/21/2022] Open
Abstract
Barley is the only crop in the Poaceae family with adhering husks at maturity. The color of husk at barely development stage could influence the agronomic traits and malting qualities of grains. A barley mutant with a white husk was discovered from the malting barley cultivar Supi 3 and designated wh (white husk). Morphological changes and the genetics of white husk barley were investigated. Husks of the mutant were white at the heading and flowering stages but yellowed at maturity. The diastatic power and α-amino nitrogen contents also significantly increased in wh mutant. Transmission electron microscopy examination showed abnormal chloroplast development in the mutant. Genetic analysis of F2 and BC1F1 populations developed from a cross of wh and Yangnongpi 5 (green husk) showed that the white husk was controlled by a single recessive gene (wh). The wh gene was initially mapped between 49.64 and 51.77 cM on chromosome 3H, which is syntenic with rice chromosome 1 where a white husk gene wlp1 has been isolated. The barley orthologous gene of wlp1 was sequenced from both parents and a 688 bp deletion identified in the wh mutant. We further fine-mapped the wh gene between SSR markers Bmac0067 and Bmag0508a with distances of 0.36 cM and 0.27 cM in an F2 population with 1115 individuals of white husk. However, the wlp1 orthologous gene was mapped outside the interval. New candidate genes were identified based on the barley genome sequence.
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Affiliation(s)
- Wei Hua
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA 6150, Australia
| | - Jinghuan Zhu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yi Shang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junmei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiaojun Jia
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qisen Zhang
- Australian Export Grain Innovation Centre, South Perth, WA 6151, Australia
| | - Jianming Yang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- * E-mail: ;
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA 6150, Australia
- * E-mail: ;
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Shan T, Pang S, Li J, Li X, Su L. Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:902. [PMID: 26541547 PMCID: PMC4635539 DOI: 10.1186/s12864-015-2184-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida. RESULTS A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region. CONCLUSIONS A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.
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Affiliation(s)
- Tifeng Shan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Shaojun Pang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Xia Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Li Su
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
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Zhou G, Zhang Q, Tan C, Zhang XQ, Li C. Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map. BMC Genomics 2015; 16:804. [PMID: 26474969 PMCID: PMC4609152 DOI: 10.1186/s12864-015-2027-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/06/2015] [Indexed: 11/17/2022] Open
Abstract
Background Development of molecular markers such as SSR (simple sequence repeat), DArT (diversity arrays technology) and SNP (single nucleotide polymorphism) is fundamental for linkage map construction and QTL mapping. However, DArT and SNP genotyping require special tools, and detection of SSR polymorphisms requires time-consuming polyacrylamide electrophoresis. Furthermore, many markers have been mapped in different populations such that their genetic positions are inconsistent. Recently, InDel (insertion and deletion) markers have become popular in genetic map construction and map-based cloning. Results Aligning genomic DNA sequences in two barley cultivars (Morex and Barke) identified 436,640 InDels. We designed 1140 InDel markers across the barley genome with an average genetic distance of 1 cM, each having a unique location in the barley genome. High-resolution melting (HRM) technology was used to genotype 55 InDel markers; those PCR amplicons with melting temperature differences >0.3 °C were ideal for HRM genotyping. The 1140 InDel markers together with 383 SSRs, 3909 gene-based SNPs and 1544 DArT markers were integrated into single barley genetic map according to their physical map positions. Conclusions High-density InDel markers with specific genome locations were developed, with 6976 molecular markers (SSRs, DArTs, SNPs and InDels) integrated into single barley genetic map. HRM genotyping of the InDel markers each with single PCR band will facilitate quick map construction and gene fine-mapping. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2027-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gaofeng Zhou
- Department of Agriculture and Food, Locked Bag 4, Bentley Delivery Centre, Bentley, WA, 6983, Australia.
| | - Qisen Zhang
- Australian Export Grains Innovation Centre, 3 Baron-Hay Court, South Perth, WA, 6155, Australia.
| | - Cong Tan
- Western Barley Genetics Alliance/Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance/Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Chengdao Li
- Western Barley Genetics Alliance/Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia.
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Kamino LN, Singh D, Pallotta MA, Collins NC, Park RF. Mapping of seedling resistance in barley to Puccinia striiformis f. sp. pseudohordei. J Appl Genet 2015. [PMID: 26198458 DOI: 10.1007/s13353-015-0304-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The barley grass stripe rust (BGYR) pathogen Puccinia striiformis f. sp. pseudohordei was first detected in Australia in 1997. While studies have established that it is virulent on wild barley grass, and can infect several barley cultivars, the basis of genetic resistance to this pathogen in barley is largely unknown. Understanding the genetic basis of host resistance and ensuring the selection of germplasm with multiple resistance genes are important to mitigate the potential impact of BGYR in barley production. Genetic analysis of seedling resistance to BGYR in two barley doubled haploid populations, Amaji Nijo/WI2585 (AN/WI) and Galleon/Haruna Nijo (GL/HN), indicated that resistance is governed by several genes. Marker regression analysis of the seedling resistance data from the AN/WI population detected a major QTL, BGYR_WI1 (resistance contributed by WI2585 with the closest marker explaining 52 % of the total phenotypic effect) on chromosome 1HS, flanked by the loci Xabg59 and Xabc310b at map positions 0.0 and 6.9 cM, respectively. Similarly, a major QTL, BGYR_HN1, (resistance contributed by Haruna Nijo with the closest marker explaining 70 % of the total phenotypic effect) was detected in the GL/HN population and was mapped to 1HS, flanked by the loci Xbcd135 and XHOR1 at map positions 12.8 and 24.5 cM, respectively. In addition, several minor loci that provided resistance against BGYR were detected in both populations. While defined QTL intervals were large, the analysis nonetheless provides new information on sources of major QTL controlling resistance to BGYR.
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Affiliation(s)
- L N Kamino
- Plant Breeding Institute (PBI), The University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - D Singh
- Plant Breeding Institute (PBI), The University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia.
| | - M A Pallotta
- Australian Centre for Plant Functional Genomics, University of Adelaide, Waite campus, Urrbrae, South Australia, 5064, Australia
| | - N C Collins
- Australian Centre for Plant Functional Genomics, University of Adelaide, Waite campus, Urrbrae, South Australia, 5064, Australia
| | - R F Park
- Plant Breeding Institute (PBI), The University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
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Zhou G, Zhang Q, Zhang XQ, Tan C, Li C. Construction of High-Density Genetic Map in Barley through Restriction-Site Associated DNA Sequencing. PLoS One 2015; 10:e0133161. [PMID: 26182149 PMCID: PMC4504713 DOI: 10.1371/journal.pone.0133161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/23/2015] [Indexed: 12/21/2022] Open
Abstract
Genetic maps in barley are usually constructed from a limited number of molecular markers such as SSR (simple sequence repeat) and DarT (diversity arrays technology). These markers must be first developed before being used for genotyping. Here, we introduce a new strategy based on sequencing progeny of a doubled haploid population from Baudin × AC Metcalfe to construct a genetic map in barley. About 13,547 polymorphic SNP tags with >93% calling rate were selected to construct the genetic map. A total of 12,998 SNP tags were anchored to seven linkage groups which spanned a cumulative 967.6 cM genetic distance. The high-density genetic map can be used for QTL mapping and the assembly of WGS and BAC contigs. The genetic map was evaluated for its effectiveness and efficiency in QTL mapping and candidate gene identification. A major QTL for plant height was mapped at 105.5 cM on chromosome 3H. This QTL with LOD value of 13.01 explained 44.5% of phenotypic variation. This strategy will enable rapid and efficient establishment of high-density genetic maps in other species.
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Affiliation(s)
- Gaofeng Zhou
- Department of Agriculture and Food, South Perth, WA, Australia
| | - Qisen Zhang
- Australian Export Grains Innovation Centre, South Perth, WA, Australia
| | - Xiao-qi Zhang
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Cong Tan
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Chengdao Li
- Department of Agriculture and Food, South Perth, WA, Australia
- Australian Export Grains Innovation Centre, South Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
- * E-mail:
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Kuczyńska A, Mikołajczak K, Ćwiek H. Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Akfirat FS, Ertugrul F, Hasancebi S, Aydin Y, Akan K, Mert Z, Cakir M, Uncuoglu AA. Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.). J Genet 2014; 92:233-40. [PMID: 23970078 DOI: 10.1007/s12041-013-0254-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have previously reported Xgwm382 as a diagnostic marker for disease resistance against yellow rust in Izgi2001 x ES14 F2 population. Among the same earlier tested 230 primers, one SSR marker (Xgwm311) also amplified a fragment which is present in the resistant parent and in the resistant bulks, but absent in the susceptible parent and in the susceptible bulks. To understand the chromosome group location of these diagnostic markers, Xgwm382 and Xgwm311, in the same population, we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1-21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F2 individuals as a diagnostic marker for yellow rust disease and provided the location of Xgwm382 and Xgwm311 on chromosome 2AL in our plant material.
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Affiliation(s)
- F Senturk Akfirat
- Department of Molecular Biology and Genetics, Gebze Institute of Technology, Cayirova Campus, 41700, Gebze, Kocaeli, Turkey
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Phylogenetic relationships between four Salix L. species based on DArT markers. Int J Mol Sci 2013; 14:24113-25. [PMID: 24336112 PMCID: PMC3876099 DOI: 10.3390/ijms141224113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 11/28/2013] [Accepted: 12/02/2013] [Indexed: 11/16/2022] Open
Abstract
The objectives of this study were to evaluate the usefulness of DArT markers in genotypic identification of willow species and describe genetic relationships between four willow species: Salix viminalis, S. purpurea, S. alba and S. triandra. The experimental plant material comprised 53 willow genotypes of these four species, which are popularly grown in Poland. DArT markers seem to identify Salix species with a high degree of accuracy. As a result, the examined species were divided into four distinct groups which corresponded to the four analyzed species. In our study, we observed that S. triandra was very different genetically from the other species, including S. alba which is generally classified into the same subgenus of Salix. The above corroborates the findings of other authors who relied on molecular methods to reveal that the classification of S. triandra to the subgenus Salix was erroneous. The Principal Coordinate Analysis (PCoA) and the neighbor-joining dendrogram also confirmed the clear division of the studied willow genotypes into four clusters corresponding to individual species. This confirmed the usefulness of DArT markers in taxonomic analyses and identification of willow species.
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Lüpken T, Stein N, Perovic D, Habekuss A, Krämer I, Hähnel U, Steuernagel B, Scholz U, Zhou R, Ariyadasa R, Taudien S, Platzer M, Martis M, Mayer K, Friedt W, Ordon F. Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1201-12. [PMID: 23456135 DOI: 10.1007/s00122-013-2047-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/13/2013] [Indexed: 05/20/2023]
Abstract
Soil-borne barley yellow mosaic virus disease, caused by different strains of Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), is one of the most important diseases of winter barley (Hordeum vulgare L.) in Europe and East Asia. The recessive resistance gene rym11 located in the centromeric region of chromosome 4HL is effective against all so far known strains of BaMMV and BaYMV in Germany. In order to isolate this gene, a high-resolution mapping population (10,204 meiotic events) has been constructed. F2 plants were screened with co-dominant flanking markers and segmental recombinant inbred lines (RILs) were tested for resistance to BaMMV under growth chamber and field conditions. Tightly linked markers were developed by exploiting (1) publicly available barley EST sequences, (2) employing barley synteny to rice, Brachypodium distachyon and sorghum and (3) using next-generation sequencing data of barley. Using this approach, the genetic interval was efficiently narrowed down from the initial 10.72 % recombination to 0.074 % recombination. A marker co-segregating with rym11 was developed providing the basis for gene isolation and efficient marker-assisted selection.
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Affiliation(s)
- Thomas Lüpken
- Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
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23
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Characterization and evolutionary analysis of Brassica species-diverged sequences containing simple repeat units. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0076-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD, KaviKishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One 2011; 6:e27275. [PMID: 22102885 PMCID: PMC3216927 DOI: 10.1371/journal.pone.0027275] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/12/2011] [Indexed: 12/17/2022] Open
Abstract
Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.
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Affiliation(s)
- Mahendar Thudi
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Bohra
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Spurthi N. Nayak
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Nicy Varghese
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Trushar M. Shah
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - R. Varma Penmetsa
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | | | - Srivani Gudipati
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M. Gaur
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pawan L. Kulwal
- State Level Biotechnology Centre, Mahatma Phule Agricultural University, Ahmednagar, India
| | - Hari D. Upadhyaya
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Günter Kahl
- Molecular BioSciences, University of Frankfurt, Frankfurt am Main, Germany
| | - Christopher D. Town
- J. Craig Venter Institute (JCVI), Rockville, Maryland, United States of America
| | | | - Douglas R. Cook
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Rajeev K. Varshney
- Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- CGIAR Generation Challenge Programme (GCP), CIMMYT, Mexico DF, Mexico
- * E-mail:
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Supriya A, Senthilvel S, Nepolean T, Eshwar K, Rajaram V, Shaw R, Hash CT, Kilian A, Yadav RC, Narasu ML. Development of a molecular linkage map of pearl millet integrating DArT and SSR markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:239-50. [PMID: 21476042 DOI: 10.1007/s00122-011-1580-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 03/21/2011] [Indexed: 05/09/2023]
Abstract
Pearl millet is an important component of food security in the semi-arid tropics and is assuming greater importance in the context of changing climate and increasing demand for highly nutritious food and feed. Molecular tools have been developed and applied for pearl millet on a limited scale. However, the existing tool kit needs to be strengthened further for its routine use in applied breeding programs. Here, we report enrichment of the pearl millet molecular linkage map by exploiting low-cost and high-throughput Diversity Arrays Technology (DArT) markers. Genomic representation from 95 diverse genotypes was used to develop a DArT array with circa 7,000 clones following PstI/BanII complexity reduction. This array was used to genotype a set of 24 diverse pearl millet inbreds and 574 polymorphic DArT markers were identified. The genetic relationships among the inbred lines as revealed by DArT genotyping were in complete agreement with the available pedigree data. Further, a mapping population of 140 F(7) Recombinant Inbred Lines (RILs) from cross H 77/833-2 × PRLT 2/89-33 was genotyped and an improved linkage map was constructed by integrating DArT and SSR marker data. This map contains 321 loci (258 DArTs and 63 SSRs) and spans 1148 cM with an average adjacent-marker interval length of 3.7 cM. The length of individual linkage groups (LGs) ranged from 78 cM (LG 3) to 370 cM (LG 2). This better-saturated map provides improved genome coverage and will be useful for genetic analyses of important quantitative traits. This DArT platform will also permit cost-effective background selection in marker-assisted backcrossing programs as well as facilitate comparative genomics and genome organization studies once DNA sequences of polymorphic DArT clones are available.
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Affiliation(s)
- A Supriya
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, India
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Cistué L, Cuesta-Marcos A, Chao S, Echávarri B, Chutimanitsakun Y, Corey A, Filichkina T, Garcia-Mariño N, Romagosa I, Hayes PM. Comparative mapping of the Oregon Wolfe Barley using doubled haploid lines derived from female and male gametes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1399-1410. [PMID: 21311855 DOI: 10.1007/s00122-011-1540-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 01/14/2011] [Indexed: 05/30/2023]
Abstract
The Oregon Wolfe Barley mapping population is a resource for genetics research and instruction. Prior reports are based on a population of doubled haploid (DH) lines developed by the Hordeum bulbosum (H.b.) method, which samples female gametes. We developed new DH lines from the same cross using anther culture (A.C.), which samples male gametes. Linkage maps were generated in each of the two subpopulations using the same 1,328 single nucleotide polymorphism markers. The linkage maps based on DH lines derived from the products of megasporogeneis and microsporogenesis revealed minor differences in terms of estimated recombination rates. There were no differences in locus ordering. There was greater segregation distortion in the A.C.-derived subpopulation than in the H.b.-derived subpopulation, but in the region showing the greatest distortion, the cause was more likely allelic variation at the ZEO1 plant height locus rather than to DH production method. The effects of segregation distortion and pleiotropy had greater impacts on estimates of quantitative trait locus effect than population size for reproductive fitness traits assayed under greenhouse conditions. The Oregon Wolfe Barley (OWB) population and data are community resources. Seed is available from three distribution centers located in North America, Europe, and Asia. Details on ordering seed sets, as well as complete genotype and phenotype data files, are available at http://wheat.pw.usda.gov/ggpages/maps/OWB/ .
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Affiliation(s)
- L Cistué
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR 97331, USA.
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Sui X, He Z, Lu Y, Wang Z, Xia X. Molecular mapping of a non-host resistance gene YrpstY1 in barley (Hordeum vulgare L.) for resistance to wheat stripe rust. Hereditas 2010; 147:176-82. [PMID: 21039455 DOI: 10.1111/j.1601-5223.2010.02169.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cultivated barley (Hordeum vulgare L.) is considered as a non-host or inappropriate host species for wheat stripe rust caused by Puccinia striiformis f. sp. tritici. Most barley cultivars show a broad-spectrum resistance to wheat stripe rust. To determine the genes for resistance to wheat stripe rust in barley, a cross was made between a resistant barley line Y12 and a susceptible line Y16. The two parents, F(1) and 147 BC(1) plants were tested at seedling stage with Chinese prevalent race CYR32 of Puccinia striiformis f. sp. tritici by artificial inoculation in greenhouse. The results indicated that Y12 possessed one dominant resistance gene to wheat stripe rust, designated YrpstY1 provisionally. A total of 388 simple sequence repeat (SSR) markers were used to map the resistance gene in Y12 using bulked segregant analysis. A linkage map, including nine SSR loci on chromosome 7H and YrpstY1, was constructed using the BC(1) population, indicating that the resistance gene YrpstY1 is located on chromosome 7H. It is potential to transfer the resistance gene into common wheat for stripe rust resistance.
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Affiliation(s)
- Xinxia Sui
- College of Life Sciences, Shandong Agricultural University, Taian, PR China
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Shavrukov Y, Gupta NK, Miyazaki J, Baho MN, Chalmers KJ, Tester M, Langridge P, Collins NC. HvNax3—a locus controlling shoot sodium exclusion derived from wild barley (Hordeum vulgare ssp. spontaneum). Funct Integr Genomics 2010; 10:277-91. [DOI: 10.1007/s10142-009-0153-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 12/03/2009] [Accepted: 12/13/2009] [Indexed: 01/17/2023]
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Leino MW, Hagenblad J. Nineteenth Century Seeds Reveal the Population Genetics of Landrace Barley (Hordeum vulgare). Mol Biol Evol 2009; 27:964-73. [DOI: 10.1093/molbev/msp308] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 2009; 10:582. [PMID: 19961604 PMCID: PMC2797026 DOI: 10.1186/1471-2164-10-582] [Citation(s) in RCA: 347] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 12/04/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. RESULTS Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. CONCLUSION The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.
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Affiliation(s)
- Timothy J Close
- Department of Botany & Plant Sciences, University of California (UCR), Riverside, CA, 92521, USA.
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Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 2009. [PMID: 19961604 DOI: 10.1186/1471‐2164‐10‐582] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. RESULTS Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. CONCLUSION The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.
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Affiliation(s)
- Timothy J Close
- Department of Botany & Plant Sciences, University of California (UCR), Riverside, CA, 92521, USA.
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Jing HC, Bayon C, Kanyuka K, Berry S, Wenzl P, Huttner E, Kilian A, Hammond-Kosack KE. DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum. BMC Genomics 2009. [PMID: 19788762 DOI: 10.1186/1471‐2164‐10‐458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Triticum monococcum (2n = 2x = 14) is an ancient diploid wheat with many useful traits and is used as a model for wheat gene discovery. DArT (Diversity Arrays Technology) employs a hybridisation-based approach to type thousands of genomic loci in parallel. DArT markers were developed for T. monococcum to assess genetic diversity, compare relationships with hexaploid genomes, and construct a genetic linkage map integrating DArT and microsatellite markers. RESULTS A DArT array, consisting of 2304 hexaploid wheat, 1536 tetraploid wheat, 1536 T. monococcum as well as 1536 T. boeoticum representative genomic clones, was used to fingerprint 16 T. monococcum accessions of diverse geographical origins. In total, 846 polymorphic DArT markers were identified, of which 317 were of T. monococcum origin, 246 of hexaploid, 157 of tetraploid, and 126 of T. boeoticum genomes. The fingerprinting data indicated that the geographic origin of T. monococcum accessions was partially correlated with their genetic variation. DArT markers could also well distinguish the genetic differences amongst a panel of 23 hexaploid wheat and nine T. monococcum genomes. For the first time, 274 DArT markers were integrated with 82 simple sequence repeat (SSR) and two morphological trait loci in a genetic map spanning 1062.72 cM in T. monococcum. Six chromosomes were represented by single linkage groups, and chromosome 4Am was formed by three linkage groups. The DArT and SSR genetic loci tended to form independent clusters along the chromosomes. Segregation distortion was observed for one third of the DArT loci. The Ba (black awn) locus was refined to a 23.2 cM region between the DArT marker locus wPt-2584 and the microsatellite locus Xgwmd33 on 1Am; and the Hl (hairy leaf) locus to a 4.0 cM region between DArT loci 376589 and 469591 on 5Am. CONCLUSION DArT is a rapid and efficient approach to develop many new molecular markers for genetic studies in T. monococcum. The constructed genetic linkage map will facilitate localisation and map-based cloning of genes of interest, comparative mapping as well as genome organisation and evolution studies between this ancient diploid species and other crops.
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Affiliation(s)
- Hai-Chun Jing
- Centre for Sustainable Pest and Disease Management, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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Jing HC, Bayon C, Kanyuka K, Berry S, Wenzl P, Huttner E, Kilian A, Hammond-Kosack KE. DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum. BMC Genomics 2009; 10:458. [PMID: 19788762 PMCID: PMC2764732 DOI: 10.1186/1471-2164-10-458] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 09/30/2009] [Indexed: 02/08/2023] Open
Abstract
Background Triticum monococcum (2n = 2x = 14) is an ancient diploid wheat with many useful traits and is used as a model for wheat gene discovery. DArT (Diversity Arrays Technology) employs a hybridisation-based approach to type thousands of genomic loci in parallel. DArT markers were developed for T. monococcum to assess genetic diversity, compare relationships with hexaploid genomes, and construct a genetic linkage map integrating DArT and microsatellite markers. Results A DArT array, consisting of 2304 hexaploid wheat, 1536 tetraploid wheat, 1536 T. monococcum as well as 1536 T. boeoticum representative genomic clones, was used to fingerprint 16 T. monococcum accessions of diverse geographical origins. In total, 846 polymorphic DArT markers were identified, of which 317 were of T. monococcum origin, 246 of hexaploid, 157 of tetraploid, and 126 of T. boeoticum genomes. The fingerprinting data indicated that the geographic origin of T. monococcum accessions was partially correlated with their genetic variation. DArT markers could also well distinguish the genetic differences amongst a panel of 23 hexaploid wheat and nine T. monococcum genomes. For the first time, 274 DArT markers were integrated with 82 simple sequence repeat (SSR) and two morphological trait loci in a genetic map spanning 1062.72 cM in T. monococcum. Six chromosomes were represented by single linkage groups, and chromosome 4Am was formed by three linkage groups. The DArT and SSR genetic loci tended to form independent clusters along the chromosomes. Segregation distortion was observed for one third of the DArT loci. The Ba (black awn) locus was refined to a 23.2 cM region between the DArT marker locus wPt-2584 and the microsatellite locus Xgwmd33 on 1Am; and the Hl (hairy leaf) locus to a 4.0 cM region between DArT loci 376589 and 469591 on 5Am. Conclusion DArT is a rapid and efficient approach to develop many new molecular markers for genetic studies in T. monococcum. The constructed genetic linkage map will facilitate localisation and map-based cloning of genes of interest, comparative mapping as well as genome organisation and evolution studies between this ancient diploid species and other crops.
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Affiliation(s)
- Hai-Chun Jing
- Centre for Sustainable Pest and Disease Management, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
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Lee HR, Bae IH, Park SW, Kim HJ, Min WK, Han JH, Kim KT, Kim BD. Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences. Mol Cells 2009; 27:21-37. [PMID: 19214431 DOI: 10.1007/s10059-009-0002-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 10/01/2008] [Accepted: 10/02/2008] [Indexed: 11/29/2022] Open
Abstract
Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.
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Affiliation(s)
- Heung-Ryul Lee
- Department of Plant Science, Seoul National University, Seoul, 151-921, Korea
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Genetic Improvement of Malting Quality through Conventional Breeding and Marker-assisted Selection. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-3-642-01279-2_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Francki MG, Walker E, Crawford AC, Broughton S, Ohm HW, Barclay I, Wilson RE, McLean R. Comparison of genetic and cytogenetic maps of hexaploid wheat (Triticum aestivum L.) using SSR and DArT markers. Mol Genet Genomics 2008. [PMID: 19020902 DOI: 10.1007/s00438‐008‐0403‐9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A number of technologies are available to increase the abundance of DNA markers and contribute to developing high resolution genetic maps suitable for genetic analysis. The aim of this study was to expand the number of Diversity Array Technology (DArT) markers on the wheat array that can be mapped in the wheat genome, and to determine their chromosomal location with respect to simple sequence repeat (SSR) markers and their position on the cytogenetic map. A total of 749 and 512 individual DArT and SSR markers, respectively, were identified on at least one of four genetic maps derived from recombinant inbred line (RIL) or doubled haploid (DH) populations. A number of clustered DArT markers were observed in each genetic map, in which 20-34% of markers were redundant. Segregation distortion of DArT and SSR markers was also observed in each mapping population. Only 14% of markers on the Version 2.0 wheat array were assigned to chromosomal bins by deletion mapping using aneuploid lines. In this regard, methylation effects need to be considered when applying DArT marker in genetic mapping. However, deletion mapping of DArT markers provides a reference to align genetic and cytogenetic maps and estimate the coverage of DNA markers across the wheat genome.
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Affiliation(s)
- Michael G Francki
- Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia.
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Francki MG, Walker E, Crawford AC, Broughton S, Ohm HW, Barclay I, Wilson RE, McLean R. Comparison of genetic and cytogenetic maps of hexaploid wheat (Triticum aestivum L.) using SSR and DArT markers. Mol Genet Genomics 2008; 281:181-91. [PMID: 19020902 DOI: 10.1007/s00438-008-0403-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 11/03/2008] [Indexed: 11/28/2022]
Abstract
A number of technologies are available to increase the abundance of DNA markers and contribute to developing high resolution genetic maps suitable for genetic analysis. The aim of this study was to expand the number of Diversity Array Technology (DArT) markers on the wheat array that can be mapped in the wheat genome, and to determine their chromosomal location with respect to simple sequence repeat (SSR) markers and their position on the cytogenetic map. A total of 749 and 512 individual DArT and SSR markers, respectively, were identified on at least one of four genetic maps derived from recombinant inbred line (RIL) or doubled haploid (DH) populations. A number of clustered DArT markers were observed in each genetic map, in which 20-34% of markers were redundant. Segregation distortion of DArT and SSR markers was also observed in each mapping population. Only 14% of markers on the Version 2.0 wheat array were assigned to chromosomal bins by deletion mapping using aneuploid lines. In this regard, methylation effects need to be considered when applying DArT marker in genetic mapping. However, deletion mapping of DArT markers provides a reference to align genetic and cytogenetic maps and estimate the coverage of DNA markers across the wheat genome.
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Affiliation(s)
- Michael G Francki
- Department of Agriculture and Food Western Australia, South Perth, WA 6151, Australia.
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A consensus map of chromosome 6R in rye (Secale cereale L.). Cell Mol Biol Lett 2008; 14:190-8. [PMID: 18979069 PMCID: PMC6275745 DOI: 10.2478/s11658-008-0042-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 07/11/2008] [Indexed: 11/21/2022] Open
Abstract
Four F(2) mapping populations derived from crosses between rye inbred lines DS2 x RXL10, 541 x Ot1-3, S120 x S76 and 544 x Ot0-20 were used to develop a consensus map of chromosome 6R. Thirteen marker loci that were polymorphic in more than one mapping population constituted the basis for the alignment of the four maps using the JoinMap v. 3.0 software package. The consensus map consists of 104 molecular marker loci including RFLPs, RAPDs, AFLPs, SSRs, ISSRs, SCARs, STSs and isozymes. The average distance between the marker loci is 1.3 cM, and the total map length is 135.5 cM. This consensus map may be used as a source of molecular markers for the rapid development of new maps of chromosome 6R in any mapping population.
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Peleg Z, Saranga Y, Suprunova T, Ronin Y, Röder MS, Kilian A, Korol AB, Fahima T. High-density genetic map of durum wheat x wild emmer wheat based on SSR and DArT markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:103-15. [PMID: 18437346 DOI: 10.1007/s00122-008-0756-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 03/26/2008] [Indexed: 05/18/2023]
Abstract
A genetic linkage map of tetraploid wheat was constructed based on a cross between durum wheat [Triticum turgidum ssp. durum (Desf.) MacKey] cultivar Langdon and wild emmer wheat [T. turgidum ssp. dicoccoides (Körn.) Thell.] accession G18-16. One hundred and fifty-two single-seed descent derived F(6) recombinant inbred lines (RILs) were analyzed with a total of 690 loci, including 197 microsatellite and 493 DArT markers. Linkage analysis defined 14 linkage groups. Most markers were mapped to the B-genome (60%), with an average of 57 markers per chromosome and the remaining 40% mapped to the A-genome, with an average of 39 markers per chromosome. To construct a stabilized (skeleton) map, markers interfering with map stability were removed. The skeleton map consisted of 307 markers with a total length of 2,317 cM and average distance of 7.5 cM between adjacent markers. The length of individual chromosomes ranged between 112 cM for chromosome 4B to 217 cM for chromosome 3B. A fraction (30.1%) of the markers deviated significantly from the expected Mendelian ratios; clusters of loci showing distorted segregation were found on chromosomes 1A, 1BL, 2BS, 3B, and 4B. DArT markers showed high proportion of clustering, which may be indicative of gene-rich regions. Three hundred and fifty-two new DArT markers were mapped for the first time on the current map. This map provides a useful groundwork for further genetic analyses of important quantitative traits, positional cloning, and marker-assisted selection, as well as for genome comparative genomics and genome organization studies in wheat and other cereals.
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Affiliation(s)
- Zvi Peleg
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Mt. Carmel, 31905 Haifa, Israel
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Gupta PK, Rustgi S, Mir RR. Array-based high-throughput DNA markers for crop improvement. Heredity (Edinb) 2008; 101:5-18. [PMID: 18461083 DOI: 10.1038/hdy.2008.35] [Citation(s) in RCA: 242] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The last two decades have witnessed a remarkable activity in the development and use of molecular markers both in animal and plant systems. This activity started with low-throughput restriction fragment length polymorphisms and culminated in recent years with single nucleotide polymorphisms (SNPs), which are abundant and uniformly distributed. Although the latter became the markers of choice for many, their discovery needed previous sequence information. However, with the availability of microarrays, SNP platforms have been developed, which allow genotyping of thousands of markers in parallel. Besides SNPs, some other novel marker systems, including single feature polymorphisms, diversity array technology and restriction site-associated DNA markers, have also been developed, where array-based assays have been utilized to provide for the desired ultra-high throughput and low cost. These microarray-based markers are the markers of choice for the future and are already being used for construction of high-density maps, quantitative trait loci (QTL) mapping (including expression QTLs) and genetic diversity analysis with a limited expense in terms of time and money. In this study, we briefly describe the characteristics of these array-based marker systems and review the work that has already been done involving development and use of these markers, not only in simple eukaryotes like yeast, but also in a variety of seed plants with simple or complex genomes.
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Affiliation(s)
- P K Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, Uttar Pradesh, India.
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