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Xue S, Hu S, Chen X, Ma Y, Lu M, Bai S, Wang X, Sun T, Wang Y, Wan H, An X, Li S. Fine mapping of Pm58 from Aegilops tauschii conferring powdery mildew resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1657-1669. [PMID: 35234985 DOI: 10.1007/s00122-022-04061-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/11/2022] [Indexed: 05/26/2023]
Abstract
The powdery mildew resistance gene Pm58 was traced to a 141.3-kb interval with the co-segregating marker Xkasp68500 in wheat breeding. Pm58 is a powdery mildew resistance gene identified in Aegilops tauschii accession TA1662 and effective in a common wheat background. To finely map Pm58, an F2 population of 676 plants derived from the cross T093 × TA1662 was used for recombinant screening. We obtained 13 recombinants that occurred between the flanking markers Xhnu670 and Xhnu186. Genotyping and phenotyping these recombinant F2:3 families delimited Pm58 to a 0.22-cM interval (Xsts20220-Xkasp61553) on chromosome arm 2DS. The region carrying the Pm58 locus was approximately 141.3-kb, which contained eight annotated genes according to the reference genome sequence of Ae. tauschii AL8/78. Haplotype analysis of 178 Ae. tauschii accessions using the candidate gene-specific markers identified a disease resistance gene AET2Gv20068500 as a candidate for Pm58. Comparative mapping of the Pm58-containing interval revealed two presence/absence variations (PAVs) between AL8/78 and common wheat Chinese Spring. PAV-1 resides in the 3'-end of AET2Gv20068500. The majority of 158 common wheat cultivars (84.8%) displayed the absence of a 14.1-kb fragment in the PAV-1 region, which was confirmed by aligning the targeted genome sequences of the other sequenced Ae. tauschii accessions and common wheat cultivars. A co-segregating marker Xkasp68500 developed from AET2Gv20068500 can distinguish TA1662 from all randomly selected common wheat cultivars and will be instrumental for tracking Pm58 in breeding programs.
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Affiliation(s)
- Shulin Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China.
| | - Shanshan Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Xian Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Yuyu Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Mingxue Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Xintian Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Tiepeng Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Yingxue Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Xia An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, 475004, Henan, China.
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Niu F, Xu Y, Liu X, Zhao L, Bernardo A, Li Y, Liu G, Chen MS, Cao L, Hu Z, Xu X, Bai G. The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2927-2935. [PMID: 32617615 DOI: 10.1007/s00122-020-03642-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/20/2020] [Indexed: 05/19/2023]
Abstract
The recessive Hessian fly resistance gene h4 and flanking SNP markers were located to a 642 kb region in chromosome 1A of the wheat cultivar 'Java.' Hessian fly (HF), Mayetiola destructor, is one of the most destructive insect pests in wheat worldwide. The wheat cultivar 'Java' was reported to carry a recessive gene (h4) for HF resistance; however, its chromosome location has not been determined. To map the HF resistance gene in Java, two populations of recombinant inbred lines (RILs) were developed from 'Bobwhite' × Java and 'Overley' × Java, respectively, and were phenotyped for responses to infestation of HF Great Plains biotype. Analysis of phenotypic data from the F1 and the RIL populations confirmed that one recessive gene conditioned HF resistance in Java. Two linkage maps were constructed using single-nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The h4 gene was mapped to the distal end of the short arm of chromosome 1A, which explained 60.4 to 70.5% of the phenotypic variation for HF resistance in the two populations. The GBS-SNPs in the h4 candidate interval were converted into Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers to eliminate the missing data points in GBS-SNPs. Using the revised maps with KASP markers, h4 was further located to a 642 kb interval (6,635,984-7,277,935 bp). The two flanking KASP markers, KASP3299 and KASP1871, as well as four other closely linked KASP markers, may be useful for pyramiding h4 with other HF resistance genes in breeding.
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Affiliation(s)
- Fuan Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Xuming Liu
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Lanfei Zhao
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Amy Bernardo
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Yaoguang Li
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Guoxia Liu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Ming-Shun Chen
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Xiangyang Xu
- Wheat, Peanut and Other Field Crops Research Unit, 1301 N. Western Rd., Stillwater, OK, 74075, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA.
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA.
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Niu F, Xu Y, Liu X, Zhao L, Bernardo A, Li Y, Liu G, Chen MS, Cao L, Hu Z, Xu X, Bai G. The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar 'Java' using genotyping-by-sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2927-2935. [PMID: 32617615 DOI: 10.1002/csc2.20148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/20/2020] [Indexed: 05/19/2023]
Abstract
The recessive Hessian fly resistance gene h4 and flanking SNP markers were located to a 642 kb region in chromosome 1A of the wheat cultivar 'Java.' Hessian fly (HF), Mayetiola destructor, is one of the most destructive insect pests in wheat worldwide. The wheat cultivar 'Java' was reported to carry a recessive gene (h4) for HF resistance; however, its chromosome location has not been determined. To map the HF resistance gene in Java, two populations of recombinant inbred lines (RILs) were developed from 'Bobwhite' × Java and 'Overley' × Java, respectively, and were phenotyped for responses to infestation of HF Great Plains biotype. Analysis of phenotypic data from the F1 and the RIL populations confirmed that one recessive gene conditioned HF resistance in Java. Two linkage maps were constructed using single-nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The h4 gene was mapped to the distal end of the short arm of chromosome 1A, which explained 60.4 to 70.5% of the phenotypic variation for HF resistance in the two populations. The GBS-SNPs in the h4 candidate interval were converted into Kompetitive Allele-Specific Polymerase Chain Reaction (KASP) markers to eliminate the missing data points in GBS-SNPs. Using the revised maps with KASP markers, h4 was further located to a 642 kb interval (6,635,984-7,277,935 bp). The two flanking KASP markers, KASP3299 and KASP1871, as well as four other closely linked KASP markers, may be useful for pyramiding h4 with other HF resistance genes in breeding.
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Affiliation(s)
- Fuan Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Yunfeng Xu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Xuming Liu
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Lanfei Zhao
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Amy Bernardo
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Yaoguang Li
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Guoxia Liu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Ming-Shun Chen
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA
| | - Xiangyang Xu
- Wheat, Peanut and Other Field Crops Research Unit, 1301 N. Western Rd., Stillwater, OK, 74075, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS, 66506, USA.
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA.
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Adylova AT, Norbekov GK, Khurshut EE, Nikitina EV, Kushanov FN. SSR analysis of the genomic DNA of perspective Uzbek hexaploid winter wheat varieties. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The objective of this study was to investigate the genetic diversity of hexaploid wheat varieties of Uzbekistan breeding using simple sequence repeat (SSR) markers. These varieties are adapted to local conditions, and can be considered as the most important supplier of genetic resources for cultivation in Uzbekistan and other countries. Microsatellite markers are now most widely used and effective classes of DNA markers for genotyping, certification and classification of plant varieties. In this paper, genotyping results of 32 hexaploid wheat domestic varieties using 144 microsatellite primer pairs are presented. Microsatellite primer pairs were chosen from literature data and 36 primer pairs (from 144) gave polymorphic well-reproducible PCR-fragments. The individual SSR spectra differing in number of amplicons were obtained for each variety. A total number of 141 alleles for 36 microsatellite loci were detected. The number of alleles per locus ranged from 2 to 6, the mean number of alleles per locus (Na) was 3 alleles. For the studied genotypes group the effective number of alleles (ne) characterizing the loci by the allele frequency, varied from 1.7 to 4.8, the mean number of alleles per locus was 2.8. The expected heterozygosity (He) ranged from 0 to 0.792, averaging 0.626, in studied wheat population. The amplified fragment sizes ranged from 93 to 552 bp. The polymorphic index content (PIC) ranged from 0 to 0.758. A dendrogram was constructed using the alleles set of microsatellite loci, reflecting the phylogenetic differences of the studied hexaploid wheat varieties. It showed that Uzbekistan breeding varieties are divided into two main clusters, which may be evidence of their common origin. A genetic formula has been developed for each Uzbek wheat variety. It can be used for identification, certification of these varieties, as well as for the selection of parental pairs in the wheat breeding programs.
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Affiliation(s)
- A. T. Adylova
- Center of Genomics and Bioinformatics of the Academy of Sciences of the Republic of Uzbekistan
| | - G. K. Norbekov
- Center of Genomics and Bioinformatics of the Academy of Sciences of the Republic of Uzbekistan
| | - E. E. Khurshut
- Center of Genomics and Bioinformatics of the Academy of Sciences of the Republic of Uzbekistan
| | - E. V. Nikitina
- Center of Genomics and Bioinformatics of the Academy of Sciences of the Republic of Uzbekistan
| | - F. N. Kushanov
- Center of Genomics and Bioinformatics of the Academy of Sciences of the Republic of Uzbekistan
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Henkrar F, El-Haddoury J, Ouabbou H, Bendaou N, Udupa SM. Genetic characterization of Moroccan and the exotic bread wheat cultivars using functional and random DNA markers linked to the agronomic traits for genomics-assisted improvement. 3 Biotech 2016; 6:97. [PMID: 28330167 PMCID: PMC4823230 DOI: 10.1007/s13205-016-0413-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 03/21/2016] [Indexed: 01/21/2023] Open
Abstract
Genetic characterization, diversity analysis and estimate of the genetic relationship among varieties using functional and random DNA markers linked to agronomic traits can provide relevant guidelines in selecting parents and designing new breeding strategies for marker-assisted wheat cultivar improvement. Here, we characterize 20 Moroccan and 19 exotic bread wheat (Triticum aestivum L.) cultivars using 47 functional and 7 linked random DNA markers associated with 21 loci of the most important traits for wheat breeding. The functional marker analysis revealed that 35, 45, and 10 % of the Moroccan cultivars, respectively have the rust resistance genes (Lr34/Yr18/Pm38), dwarfing genes (Rht1b or Rht2b alleles) and the leaf rust resistance gene (Lr68). The marker alleles for genes Lr37/Yr17/Sr38, Sr24 and Yr36 were present only in the exotic cultivars and absent in Moroccan cultivars. 25 % of cultivars had 1BL.1RS translocation. 70 % of the wheat cultivars had Ppo-D1a and Ppo-A1b associated with low polyphenol oxidase activity. 10 % of cultivars showed presence of a random DNA marker allele (175 bp) linked to Hessian fly resistance gene H22. The majority of the Moroccan cultivars were carrying alleles that impart good bread making quality. Neighbor joining (NJ) and principal coordinate analysis based on the marker data revealed a clear differentiation between elite Moroccan and exotic wheat cultivars. The results of this study are useful for selecting suitable parents for making targeted crosses in marker-assisted wheat breeding and enhancing genetic diversity in the wheat cultivars.
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Affiliation(s)
- Fatima Henkrar
- ICARDA-INRA Cooperative Research Project, International Center for Agricultural Research in the Dry Areas (ICARDA), B.P. 6299, Rabat, Morocco
- Institut National de la Recherche Agronomique (INRA), B.P. 415, Rabat, Morocco
- Institut National de la Recherche Agronomique (INRA), B.P. 589, Settat, Morocco
- Laboratoire de Physiologie et Biotechnologie Végétale, Faculté des Sciences, Université Mohammed V, B.P. 1014, Rabat, Morocco
| | - Jamal El-Haddoury
- Institut National de la Recherche Agronomique (INRA), B.P. 589, Settat, Morocco
| | - Hassan Ouabbou
- Institut National de la Recherche Agronomique (INRA), B.P. 589, Settat, Morocco
| | - Najib Bendaou
- Laboratoire de Physiologie et Biotechnologie Végétale, Faculté des Sciences, Université Mohammed V, B.P. 1014, Rabat, Morocco
| | - Sripada M Udupa
- ICARDA-INRA Cooperative Research Project, International Center for Agricultural Research in the Dry Areas (ICARDA), B.P. 6299, Rabat, Morocco.
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Li C, Chen M, Chao S, Yu J, Bai G. Identification of a novel gene, H34, in wheat using recombinant inbred lines and single nucleotide polymorphism markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2065-71. [PMID: 23689741 DOI: 10.1007/s00122-013-2118-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 05/08/2013] [Indexed: 05/03/2023]
Abstract
Hessian fly (HF), Mayetiola destructor, is an important pest of wheat (Triticum aestivum L.) worldwide. Because it has multiple biotypes that are virulent to different wheat HF resistance genes, pyramiding multiple resistance genes in a cultivar can improve resistance durability, and finding DNA markers tightly linked to these genes is essential to this process. This study identified quantitative trait loci (QTLs) for Hessian fly resistance (HFR) in the wheat cultivar 'Clark' and tightly linked DNA markers for the QTLs. A linkage map was constructed with single nucleotide polymorphism and simple sequence repeat markers using a population of recombinant inbred lines (RILs) derived from the cross 'Ning7840' × 'Clark' by single-seed descent. Two QTLs associated with resistance to fly biotype GP were identified on chromosomes 6B and 1A, with the resistance alleles contributed from 'Clark'. The QTL on 6B flanked by loci Xsnp921 and Xsnp2745 explained about 37.2 % of the phenotypic variation, and the QTL on 1A was flanked by Xgwm33 and Xsnp5150 and accounted for 13.3 % of phenotypic variation for HFR. The QTL on 6B has not been reported before and represents a novel wheat gene with resistance to HF, thus, it is designated H34. A significant positive epistasis was detected between the two QTLs that accounted for about 9.5 % of the mean phenotypic variation and increased HFR by 0.16. Our results indicated that different QTLs may contribute different degrees of resistance in a cultivar and that epistasis may play an important role in HFR.
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Affiliation(s)
- Chunlian Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
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Tan CT, Carver BF, Chen MS, Gu YQ, Yan L. Genetic association of OPR genes with resistance to Hessian fly in hexaploid wheat. BMC Genomics 2013; 14:369. [PMID: 23724909 PMCID: PMC3674912 DOI: 10.1186/1471-2164-14-369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/17/2013] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Hessian fly (Mayetiola destructor) is one of the most destructive pests of wheat. The genes encoding 12-oxo-phytodienoic acid reductase (OPR) and lipoxygenase (LOX) play critical roles in insect resistance pathways in higher plants, but little is known about genes controlling resistance to Hessian fly in wheat. RESULTS In this study, 154 F6:8 recombinant inbred lines (RILs) generated from a cross between two cultivars, 'Jagger' and '2174' of hexaploid wheat (2n = 6 × =42; AABBDD), were used to map genes associated with resistance to Hessian fly. Two QTLs were identified. The first one was a major QTL on chromosome 1A (QHf.osu-1A), which explained 70% of the total phenotypic variation. The resistant allele at this locus in cultivar 2174 could be orthologous to one or more of the previously mapped resistance genes (H9, H10, H11, H16, and H17) in tetraploid wheat. The second QTL was a minor QTL on chromosome 2A (QHf.osu-2A), which accounted for 18% of the total phenotypic variation. The resistant allele at this locus in 2174 is collinear to an Yr17-containing-fragment translocated from chromosome 2N of Triticum ventricosum (2n = 4 × =28; DDNN) in Jagger. Genetic mapping results showed that two OPR genes, TaOPR1-A and TaOPR2-A, were tightly associated with QHf.osu-1A and QHf.osu-2A, respectively. Another OPR gene and three LOX genes were mapped but not associated with Hessian fly resistance in the segregating population. CONCLUSIONS This study has located two major QTLs/genes in bread wheat that can be directly used in wheat breeding programs and has also provided insights for the genetic association and disassociation of Hessian fly resistance with OPR and LOX genes in wheat.
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Affiliation(s)
- Chor Tee Tan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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Lee TG, Hong MJ, Johnson JW, Bland DE, Kim DY, Seo YW. Development and functional assessment of EST-derived 2RL-specific markers for 2BS.2RL translocations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:663-673. [PMID: 19543880 DOI: 10.1007/s00122-009-1077-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 05/15/2009] [Indexed: 05/26/2023]
Abstract
ESTs-derived markers are useful for comparative genomic analysis and can also serve as phenotype-linked functional markers. Here, we report the development of EST-derived 2RL-specific markers and the evaluation of the possibility of functional assessment of markers tagging 2RL, which carries Hessian fly resistance genes (loci). To identify transcripts specific to 2RL, unigene sequences in combination with wheat progenitor genomes were used. Total 275 contigs mapped to the long arms of homoeologous group 2 chromosomes were downloaded. To obtain a cluster corresponding to each of the wheat 275 contigs, unigene sequences of wheat, rice, barley, and rye were pooled for cross-species clusters. Out of 275 clusters examined, it was possible to design 112 cross-species primer pairs for genome-specific amplifications. Out of 112 cross-species primer pairs, 45 primer pairs (40%) produced amplicons from at least one species (three wheat progenitors or rye). Among the 45 contigs, 73% were associated with one of known functions and 82% of the contigs associated with known functions were also associated with one of the GO categories. On the basis of the oligonucleotide sequence alignment of each of 45 genome-specific amplifications, 21 amplifications (47%) were suitable for designing RR genome-specific primers, which are specific to translocated rye chromatin 2RL. Six primer pairs (13%) successfully produced amplicons in the 2BS.2RL translocation lines and not in the non-2RLs. Functional assessment of one of the 2RL-specific markers, NSFT03P2_Contig4445, was performed on Hessian fly infested NILs. Under Hessian fly infestation, significantly high expression of a gene tagged by a 2RL-specific marker (NSFT03P2_Contig4445) was observed 1 day after infestation. EST-derived 2RL-specific marker development from this study provides a basis for the development of ESTs-derived markers for detecting wheat-rye translocations. In addition, these markers could be employed in elucidating functional analysis of genes on 2RL.
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Affiliation(s)
- Tong Geon Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
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