Allele mining and haplotype discovery in barley candidate genes for drought tolerance     

András Cseri  Mátyás Cserháti  Maria von Korff  Bettina Nagy  Gábor V. Horváth  András Palágyi  János Pauk  Dénes Dudits  Ottó Törjék 《Euphytica》2011,181(3):341-356

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.  相似文献   

Impact of epistasis and QTL × environmental interaction on the oil filling rate of soybean seed at different developmental stages     

Zhenfeng Jiang  Binbin Zhang  Weili Teng  Yingpeng Han  Xue Zhao  Desheng Sun  Zhongchen Zhang  Wenbin Li 《Euphytica》2011,177(3):431-442

The oil accumulation in the developing soybean seed has been shown to be a dynamic process with different rates and activities at different phases affected by both genotype and environment. The objective of the present study was to investigate additive, epistatic and quantitative trait loci (QTL) × environment interaction (QE) effects of the QTL controlling oil filling rate in soybean seed. A total of 143 recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were used in this study to obtain 2 years of field data (2004 and 2005). A total of 26 QTL with significantly unconditional and conditional additive (a) effect and/or additive × environment interaction (ae) effect at different filling stages were identified on 14 linkage groups. Among the QTL with significant a effects, 18 QTL showed positive effects and 6 QTL had negative effects on seed filling rate of oil content during seed development. A total of 29 epistatic pairwise QTL underlying seed filling rate were identified at different filling stages. About 28 pairs of the QTL showed additive × additive epistatic (aa) effects and 14 pairs of the QTL showed aa × environment interaction (aae) effects at different filling stages. QTL with aa and aae (additive × additive × environment) effects appeared to vary at different filling stages. Our results demonstrated that oil filling rate in soybean seed were under genetic, developmental and environmental control.  相似文献   

Molecular genetics of race non-specific rust resistance in wheat   总被引：1，自引：0，他引：1  

Evans S. Lagudah 《Euphytica》2011,179(1):81-91

Over 150 resistance genes that confer resistance to either leaf rust, stripe rust or stem rust have been catalogued in wheat or introgressed into wheat from related species. A few of these genes from the ‘slow-rusting’ adult plant resistance (APR) class confer partial resistance in a race non-specific manner to one or multiple rust diseases. The recent cloning of two of these genes, Lr34/Yr18, a dual APR for leaf rust and stripe rust, and Yr36, a stripe rust APR gene, showed that they differ from other classes of plant resistance genes. Currently, seven Lr34/Yr18 haplotypes have been identified from sequencing the encoding ATP Binding Cassette transporter gene from diverse wheat germplasm of which one haplotype is commonly associated with the resistance phenotype. The paucity of well characterised APR genes, particularly for stem rust, calls for a focused effort in developing critical genetic stocks to delineate quantitative trait loci, construct specific BAC libraries for targeted APR genes to facilitate robust marker development for breeding applications, and the eventual cloning of the encoding genes.  相似文献   

Development of simple PCR-based markers linked to the <Emphasis Type="Italic">Ms</Emphasis> locus,a restorer-of-fertility gene in onion (<Emphasis Type="Italic">Allium cepa</Emphasis> L.)     

Haejeen Bang  Dong Youn Cho  Kil-Sun Yoo  Moo-Kyoung Yoon  Bhimanagouda S. Patil  Sunggil Kim 《Euphytica》2011,179(3):439-449

In order to implement reliable marker-assisted selection systems for the restorer-of-fertility locus (Ms) in onions (Allium cepa L.), simple PCR-based codominant markers linked to the Ms locus were developed. Based on the EST probe sequences of previously reported RFLP markers, full-length genomic sequences of the gene encoding putative oligopeptide transporter (OPT) was obtained by RACE. The first intron contained two 108 and 439-bp indel polymorphisms between the two Ms allele-linked OPT alleles. A simple PCR marker for OPT was developed by designing a primer pair on the flanking regions of the 108-bp indel which is created by two tandem repeats. The second simple PCR marker was developed from the EST probe encoding photosystem I subunit O (PsaO). Two 14 and 39-bp tandem repeats were identified from the 5′ upstream sequences of the PsaO-coding gene, which were isolated by genome walking. Three different compositions of these tandem repeats were identified from diverse onion germplasm. A primer set binding to the flanking sequence of these polymorphic repeats was used to amplify three different marker haplotypes. The OPT marker was tightly linked to the Ms locus at a distance of 1.5 cM, but the analysis of the linkage relationship showed little linkage disequilibrium between the marker and the Ms locus. Even so, these simple PCR markers are valuable tools for the marker-assisted selection of segregating individuals in onion F₁ hybrid breeding programs.  相似文献   

Identification of QTLs for phenolic compounds in oilseed rape (<Emphasis Type="Italic">Brassica napus L.</Emphasis>) by association mapping using SSR markers     

Abbas Rezaeizad  Benjamin Wittkop  Rod Snowdon  Maen Hasan  Valiollah Mohammadi  Abbas Zali  Wolfgang Friedt 《Euphytica》2011,177(3):335-342

Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. In this study, association mapping was performed to detect QTL-linked and genome wide SSR markers linked to phenolic compounds of extraction meal in a population of 49 genetically diverse oilseed rape cultivars of dark-seeded, winter-type oilseed rape accessions. Correction for population structure was performed using 559 genome wide SSR markers. Results showed that seed colour is an important contributor to seed meal quality. Totally, 52 SSR markers linked to phenolic compounds were detected, five of them being QTL linked markers. Some of these markers were already mapped on Brassica napus chromosomes that contain known QTL controlling oilseed rape meal quality traits. Our results demonstrate that association mapping is a useful approach to complement and enhance previous QTL information for marker-assisted selection.  相似文献   

Sub-arm location of prolamin and EST-SSR loci on chromosome 1H<Superscript>ch</Superscript> from <Emphasis Type="Italic">Hordeum chilense</Emphasis>     

Salim Cherif-Mouaki  Mahmoud Said  Juan B. Alvarez  Adoración Cabrera 《Euphytica》2011,178(1):63-69

Hordeum chilense Roem. et Schult. is a diploid wild South American barley that contains genes of interest for cereal breeding, many of them located on chromosome 1H^ch. In the current study, two H. chilense-wheat addition lines with deletions in the 1H^ch chromosome were used for sub-arm localization of five prolamin (glutenin and gliadin) loci and 33 EST-SSR marker loci on chromosome 1H^ch. The two sets of markers were distributed across five sub-arm chromosome regions. Three glutenin loci (Glu-H ^ch 2, Glu-H ^ch 3, Glu-H ^ch 4) together with the gliadin locus Gli-H ^ch 1 were located on the distal 20% of the 1H^chS arm, whereas the glutenin locus Glu-H ^ch 1 was on the proximal 88% region of 1H^chL. Among 33 EST-SSR marker loci, 7 (21.2%) were on the 1H^chS arm and, of them, 3 (9.1%) were on the distal 20% end and 4 (12.1%) on the proximal 80% region. The 26 loci (78.8%) on 1H^chL were distributed across three different regions: 18 (78.8%) in the proximal 88%, 3 (9.1%) in the distal 12% and 5 (15.2%) in a region less than 12% from the distal end. The deletions in the 1H^ch chromosome added to the common wheat background were thus shown to be useful for determining the sub-arm location of EST-SSR and prolamin loci. This could facilitate the identification of molecular markers linked to genes of agronomic interest and the isolation of such genes for use in common wheat improvement.  相似文献   

Genetic analysis and associated SRAP markers for flowering traits of chrysanthemum (<Emphasis Type="Italic">Chrysanthemum morifolium</Emphasis>)     

Fei Zhang  Sumei Chen  Fadi Chen  Weimin Fang  Yanming Deng  Qingshan Chang  Pusheng Liu 《Euphytica》2011,177(1):15-24

The inheritance of two flowering traits of chrysanthemum, initial blooming time and the duration of flowering, was investigated using segregation within an F ₁ population derived from a cross between the autumn-flowering ‘Yuhualuoying’ and the summer-flowering ‘Aoyunhanxiao’ cultivars. The analysis, based on a single segregating generation and the major gene plus polygene mixed inheritance model, showed that the inheritance of both traits was compatible with the presence of two pairs of major genes displaying additivity–dominance–epistasis, with additivity predominating. As the heritability of both pairs of major genes was high (initial blooming time ~65%, duration of flowering ~72%), it should be possible to select for both traits in early breeding generations. A marker-trait association analysis based on sequence-related amplified polymorphism (SRAP) genotyping uncovered 10 (initial blooming time) and 12 (duration of flowering) markers significantly associated with phenotype, cumulatively explaining, respectively, 46 and 54% of the variation. Some potentially useful markers were identified.  相似文献   

Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes   总被引：2，自引：0，他引：2  

Zhao-ming Qi  Qiong Wu  Xue Han  Ya-nan Sun  Xiang-yu Du  Chun-yan Liu  Hong-wei Jiang  Guo-hua Hu  Qing-shan Chen 《Euphytica》2011,179(3):499-514

Oil content of soybean was a valuable quantitative trait controlled by multiple genes. Eleven QTLs were detected by both CIM and MIM method with the population crossed between Charleston and Dong nong594 in recent 3 years (2007, 2008, 2009). Combining the QTLs collected over the past 20 years, an integrated map of oil-content major QTLs in soybean was established using soymap2, which was published in 2004, as a reference. Using the software BioMercator ver.2.1, QTLs were projected from their own maps onto the reference map. In total, ninety-eight QTLs were integrated into soymap2. A meta-analysis method was used to narrow down the confidence interval, and 20 consensus QTLs and their corresponding markers were obtained. Using a local version of GENSCAN, 10,137 sequences in the consensus QTL intervals were predicted. With BLAST, these predicted genes were compared to the International Protein Index database to mine the related genes. The results offer a basis for gene mining and molecular breeding in soybean.  相似文献   

Construction of a crop—wild hybrid population for broadening genetic diversity in cultivated sunflower and first evaluation of its combining ability: the concept of neodomestication     

Hamidreza Nooryazdan  Hervé Serieys  Jacques David  Roberto Bacilieri  André J. Bervillé 《Euphytica》2011,178(2):159-175

The genetic base of sunflower elite lines is very narrow, due to many years of selection and breeding. To broaden the genetic diversity of the cultivated sunflower, in 1995 73 wild sunflower populations were crossed with 3 cultivated lines (Testers), and 219 hybrid offspring’s were evaluated in the field. GCA and SCA effects were computed suggesting for all traits a genetic potential for improvement through selection. Study of the hybrids revealed that the wild accessions bear different genetic abilities to combine with the testers for traits of morphological architecture, phenology and yield (seed weight and seed oil). The variance due to GCA and SCA showed that gene action was additive for days to flowering, branching and plant height. Genotypes derived from the same geographic origin may have either good or poor general combing ability. The correlation between GCA and per se genotype performance was positive for all traits except for seed oil content. This was the first attempt to evaluate wild-cultivated hybrids in sunflower on a large scale and will be the starting point for the management of hybrid Helianthus annuus populations for breeding. GCA and SCA estimations will facilitate the definition of strategies to manage and exploit the natural diversity for this crop.  相似文献   

Allelic changes in bread wheat cultivars were associated with long-term wheat trait improvements     

Yong-Bi Fu  Daryl J. Somers 《Euphytica》2011,179(2):209-225

Genetic impacts under selective breeding of agricultural crops have been frequently investigated with molecular tools, but inadequate attention has been paid to assess genetic changes under long-term genetic improvement of plant traits. Here we analyzed allelic changes with respect to wheat trait improvement in 78 Canadian hard red spring wheat cultivars released from 1845 to 2004 and screened with 370 mapped SSR markers. The improvements in quality, maturity, yield, disease, stem rust, leaf rust, sawfly resistance, and agronomy were considered. A total of 154 (out of 370) loci with significant allelic changes across 21 chromosomes were detected in the 78 wheat cultivars separated into improved versus non-improved groups for eight traits. The number of significant loci for improving a trait ranged from four for quality to 68 for yield and averaged 35. Many more loci with significant allelic reduction for improving a trait were detected than those with significant allelic increase. Selection for early maturity introduced more alleles, but improving the other traits purged more alleles. Significantly lower numbers of unique alleles were found in the cultivars with improved traits. The distributions of unique allele counts also varied greatly across the 21 chromosomes with respect to trait improvement. Significant SSR variation between two cultivar groups was observed for improvement in seven traits, but not in stem rust. The proportional SSR variation residing between two groups ranged from 0.014 to 0.118. The proportional SSR variations within the improved cultivar groups consistently were much lower than those within the non-improved groups. These findings clearly demonstrate the association between allelic changes and wheat trait improvements and are useful for understanding the genetic modification of the wheat genome by long-term wheat breeding.  相似文献