Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat (Triticum aestivum L.).
Ontology highlight
ABSTRACT:
SUBMITTER: Kumar A
PROVIDER: S-EPMC7415061 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.
| S-EPMC6822720 | biostudies-literature
Project description:Grain traits are important agronomic attributes with the market value as well as milling yield of bread wheat. In the present study, quantitative trait loci (QTL) regulating grain traits in wheat were identified. Data for grain area size (GAS), grain width (GWid), factor form density (FFD), grain length-width ratio (GLWR), thousand grain weight (TGW), grain perimeter length (GPL) and grain length (GL) were recorded on a recombinant inbred line derived from the cross of NW1014 × HUW468 at Meerut and Varanasi locations. A linkage map of 55 simple sequence repeat markers for 8 wheat chromosomes was used for QTL analysis by Composite interval mapping. Eighteen QTLs distributed on 8 chromosomes were identified for seven grain traits. Of these, five QTLs for GLWR were found on chromosomes 1A, 6A, 2B, and 7B, three QTLs for GPL were located on chromosomes 4A, 5A and 7B and three QTLs for GAS were mapped on 5D and 7D. Two QTLs were identified on chromosomes 4A and 5A for GL and two QTLs for GWid were identified on chromosomes 7D and 6A. Similarly, two QTLs for FFD were found on chromosomes 1A and 5D. A solitary QTL for TGW was identified on chromosome 2B. For several traits, QTLs were also co-localized on chromosomes 2B, 4A, 5A, 6A, 5D, 7B and 7D. The QTLs detected in the present study may be validated for specific crosses and then used for marker-assisted selection to improve grain quality in bread wheat.
| S-EPMC6103944 | biostudies-literature
Project description:Wheat is one of the most important food crops in the world and drought can severely impact on wheat productivity. The identification and deployment of genes for improved water use efficiency (WUE) can help alleviate yield loss under water limitation. In this study, a high-density genetic linkage map of wheat recombinant inbred lines (Ningchun 4 x Ningchun 27) containing 8751 specific locus amplified fragment (SLAF) tags (including 14757 SNPs), with a total map distance of 1685 cM and an average inter-marker map distance of 0.19 cM was constructed by SLAF-seq technology. The economic yield WUE and nine related traits under three water treatments was monitored over four years. The results showed that loci conditioning WUE were also associated with grain carbon isotope discrimination (CID), flag leaf chlorophyll content, plant height, 1000-grain weight, grain weight per spike and grain number per spike. One locus on chromosome 2B explained 26.3% WUE variation in multiple environments. Under good soil moisture conditions before flowering, the high CID genotype QWue.acn-2B Ningchun 27, was associated with WUE, high grain weight per spike, and kilo-grain weight. Under rain-fed conditions, the low CID genotype QWue.acn-2B Ningchun 4 tended to maintain more spike number and was associated with improved WUE and yield. The introduction of good chromosome fragments of QWue.acn-2B into elite lines by molecular marker assisted selection will boost up the cultivation of high-yield and water-saving wheat varieties.
| S-EPMC9879270 | biostudies-literature
Project description:In wheat, meta-QTLs (MQTLs), ortho-MQTLs, and candidate genes (CGs) were identified for nitrogen use efficiency and root system architecture. For this purpose, 1788 QTLs were available from 24 studies published during 2006-2020. Of these, 1098 QTLs were projected onto the consensus map resulting in 118 MQTLs. The average confidence interval (CI) of MQTLs was reduced up to 8.56 folds in comparison to the average CI of QTLs. Of the 118 MQTLs, 112 were anchored to the physical map of the wheat reference genome. The physical interval of MQTLs ranged from 0.02 to 666.18 Mb with a mean of 94.36 Mb. Eighty-eight of these 112 MQTLs were verified by marker-trait associations (MTAs) identified in published genome-wide association studies (GWAS); the MQTLs that were verified using GWAS also included 9 most robust MQTLs, which are particularly useful for breeders; we call them 'Breeder's QTLs'. Some selected wheat MQTLs were further utilized for the identification of ortho-MQTLs for wheat and maize; 9 such ortho-MQTLs were available. As many as 1991 candidate genes (CGs) were also detected, which included 930 CGs with an expression level of > 2 transcripts per million in relevant organs/tissues. Among the CGs, 97 CGs with functions previously reported as important for the traits under study were selected. Based on homology analysis and expression patterns, 49 orthologues of 35 rice genes were also identified in MQTL regions. The results of the present study may prove useful for the improvement of selection strategy for yield potential, stability, and performance under N-limiting conditions.Supplementary informationThe online version contains supplementary material available at 10.1007/s12298-021-01085-0.
| S-EPMC8526679 | biostudies-literature
Project description:Tolerance to metribuzin, a broad-spectrum herbicide, is an important trait for weed control in wheat breeding. However, the genetics of metribuzin tolerance in relation to the underlying quantitative trait loci (QTL) and genes is limited. This study developed F8 recombinant inbred lines (RILs) from a cross between a highly resistant genotype (Chuan Mai 25) and highly susceptible genotype (Ritchie), which were used for QTL mapping of metribuzin tolerance. Genotyping was done using a diversity arrays technology sequencing (DArTseq) platform, and phenotyping was done in controlled environments. Herbicide tolerance was measured using three traits, visual score (VS), reduction of chlorophyll content (RCC), and mean value of chlorophyll content for metribuzin-treated plants (MCC). A high-density genetic linkage map was constructed using 2,129 DArTseq markers. Inclusive composite interval mapping (ICIM) identified seven QTL, one each on chromosomes 2A, 2D, 3A, 3B, 4A, 5A, and 6A. Three major QTL-Qrcc.uwa.2AS, Qrcc.uwa.5AL, and Qrcc.uwa.6AL-explained 11.39%, 11.06%, and 11.45% of the phenotypic variation, respectively. The 5A QTL was further validated using kompetitive allele-specific PCR (KASP) assays in an F3 validation population developed from Chuan Mai 25 × Dagger. Blasting the single-nucleotide polymorphisms (SNPs) flanking the QTL in the wheat reference genome RefV1.0 revealed SNP markers within or very close to annotated genes which could be candidate genes responsible for metribuzin tolerance. Most of the candidate genes were related to metabolic detoxification, especially those of P450 pathway and xenobiotic transmembrane transporter activity, which are reportedly key molecules responsible for herbicide tolerance. This study is the first to use specially developed populations to conduct QTL mapping on the metribuzin tolerance trait. The three major QTL and candidate genes identified in this study could facilitate marker-assisted metribuzin breeding in wheat. The QTL could be fine-mapped to locate the genes responsible for metribuzin tolerance, which could be introgressed into elite wheat cultivars.
| S-EPMC7527527 | biostudies-literature
Project description:Manipulation of flowering time for adaptation through natural or genetic approaches may combat heat-stress damage that occurs at the reproductive stages in production conditions. HD2733, a popular wheat variety of the eastern plains of India, is largely sensitive to heat stress. Therefore, the current study aims to improve heat tolerance of HD2733 by introgression of QTLs associated with early anthesis and high kernel weight linked to markers Xbarc186 and Xgwm190, respectively, through marker-assisted backcross breeding (MABB) from a tolerant donor, WH730. A total of 124 simple sequence repeat (SSR) markers distributed evenly across the genome were used for the background selection. The alleles of Xbarc186 and Xgwm190 were fixed in BC2F1 and BC1F2 generations by selecting individual plants heterozygous for both marker loci and backcrossed with HD2733 and simultaneously selfed to generate BC2F1 and BC1F2 populations, respectively. Furthermore, the selected BC1F2 were selfed to generate the BC1F4 population. By background screening, a total of 39 BC2F3 and 21 BC1F4 families homozygous for the targeted QTLs with 90.9-97.9% and 86.8-88.3% RPG recoveries were selected. The best performing 17 BC2F3 and 10 BC1F4 lines were evaluated for various morpho-physiological traits. Phenotypic evaluation and multi-location trials of the introgressed lines under late sown conditions led to the selection of three promising lines with early anthesis and higher grain yield. The improved lines will serve as an excellent genetic material for functional genomics and expression studies to understand the molecular mechanisms and pathways underlying the stress tolerance.
| S-EPMC9785257 | biostudies-literature
Project description:Drought is one of the most important yield-limiting factors in Morocco. Identification and deployment of drought-tolerant wheat varieties are important to cope with the challenge of terminal moisture stress and increase wheat productivity. A panel composed of 200 elite spring bread wheat genotypes was phenotyped for yield and agronomic traits for 2 years (2020 and 2021) in Morocco under rainfed and irrigated environments. The panel was genotyped using 20K SNPs and, after filtration, a total of 15,735 SNP markers were used for a genome-wide association study (GWAS) using a mixed linear model (MLM) to identify marker-trait associations (MTA) and putative genes associated with grain yield and yield-related traits under rainfed and irrigated conditions. Significant differences were observed among the elite genotypes for grain yield and yield-related traits. Grain yield performance ranged from 0.97 to 6.16 t/ha under rainfed conditions at Sidi Al-Aidi station and from 3.31 to 9.38 t/h under irrigated conditions at Sidi Al-Aidi station, while Grain yield at Merchouch station ranged from 2.32 to 6.16 t/h under rainfed condition. A total of 159 MTAs (p < 0.001) and 46 genes were discovered, with 67 MTAs recorded under rainfed conditions and 37 MTAs recorded under irrigated conditions at the Sidi Al-Aidi station, while 55 MTAs were recorded under rainfed conditions at Merchouch station. The marker 'BobWhite_c2988_493' on chromosome 2B was significantly correlated with grain yield under rainfed conditions. Under irrigated conditions, the marker 'AX-94653560' on chromosome 2D was significantly correlated with grain yield at Sidi Al-Aidi station. The maker 'RAC875_c17918_321' located on chromosome 4A, associated with grain yield was linked with the gene TraesCS4A02G322700, which encodes for F-box domain-containing protein. The markers and candidate genes discovered in this study should be further validated for their potential use in marker-assisted selection to generate high-yielding wheat genotypes with drought tolerance.
| S-EPMC9611990 | biostudies-literature
Project description:Trichome plays an important role in heat dissipation, cold resistance, water absorption, protection of leaves from mechanical damage, and direct exposure to ultraviolet rays. It also plays an important role in the photosynthesis, transpiration, and respiration of plants. However, the genetic basis of trichome traits is not fully understood in wheat. In this study, wheat DH population (Hanxuan 10 × Lumai 14) was used to map quantitative trait loci (QTL) for trichome traits in different parts of flag leaf at 10 days after anther with growing in Zhao County, Hebei Province, and Taigu County, Shanxi Province, respectively. The results showed that trichome density (TD) was leaf center > leaf tip > leaf base and near vein > middle > edge, respectively, in both environments. The trichome length (TL) was leaf tip > leaf center > leaf base and edge > middle > near vein. Significant phenotypic positive correlations were observed between the trichome-related traits of different parts. A total of 83 QTLs for trichome-related traits were mapped onto 18 chromosomes, and each one accounted for 2.41 to 27.99% of the phenotypic variations. Two QTL hotspots were detected in two marker intervals: AX-95232910~AX-95658735 on 3A and AX-94850949~AX-109507404 on 7D. Six possible candidate genes (TraesCS3A02G406000, TraesCS3A02G414900, TraesCS3A02G440900, TraesCS7D02G145200, TraesCS7D02G149200, and TraesCS7D02G152400) for trichome-related traits of wheat leaves were screened out according to their predicted expression levels in wheat leaves. The expression of these genes may be induced by a variety of abiotic stresses. The results provide the basis for further validation and functional characterization of the candidate genes.
| S-EPMC10815787 | biostudies-literature
Project description:SET domain genes (SDGs) that are involved in histone methylation have been examined in many plant species, but have never been examined in bread wheat; the histone methylation caused due to SDGs is associated with regulation of gene expression at the transcription level. We identified a total of 166 bread wheat TaSDGs, which carry some interesting features including the occurrence of tandem/interspersed duplications, SSRs (simple sequence repeats), transposable elements, lncRNAs and targets for miRNAs along their lengths and transcription factor binding sites (TFBS) in the promoter regions. Only 130 TaSDGs encoded proteins with complete SET domain, the remaining 36 proteins had truncated SET domain. The TaSDG encoded proteins were classified into six classes (I-V and VII). In silico expression analysis indicated relatively higher expression (FPKM?>?20) of eight of the 130 TaSDGs in different tissues, and downregulation of 30 TaSDGs under heat and drought at the seedling stage. qRT-PCR was also conducted to validate the expression of seven genes at the seedling stage in pairs of contrasting genotypes in response to abiotic stresses (water and heat) and biotic stress (leaf rust). These genes were generally downregulated in response to the three stresses examined.
| S-EPMC7471321 | biostudies-literature
Project description:Meta-QTL analysis for thermotolerance in wheat was conducted to identify robust meta-QTLs (MQTLs). In this study, 441 QTLs related to 31 heat-responsive traits were projected on the consensus map with 50,310 markers. This exercise resulted in the identification of 85 MQTLs with confidence interval (CI) ranging from 0.11 to 34.9 cM with an average of 5.6 cM. This amounted to a 2.96-fold reduction relative to the mean CI (16.5 cM) of the QTLs used. Seventy-seven (77) of these MQTLs were also compared and verified with the results of recent genome-wide association studies (GWAS). The 85 MQTLs included seven MQTLs that are particularly useful for breeding purposes (we called them breeders' MQTLs). Seven ortho-MQTLs between wheat and rice genomes were also identified using synteny and collinearity. The MQTLs were used for the identification of 1,704 candidate genes (CGs). In silico expression analysis of these CGs permitted identification of 182 differentially expressed genes (DEGs), which included 36 high confidence CGs with known functions previously reported to be important for thermotolerance. These high confidence CGs encoded proteins belonging to the following families: protein kinase, WD40 repeat, glycosyltransferase, ribosomal protein, SNARE associated Golgi protein, GDSL lipase/esterase, SANT/Myb domain, K homology domain, etc. Thus, the present study resulted in the identification of MQTLs (including breeders' MQTLs), ortho-MQTLs, and underlying CGs, which could prove useful not only for molecular breeding for the development of thermotolerant wheat cultivars but also for future studies focused on understanding the molecular basis of thermotolerance.Supplementary informationThe online version contains supplementary material available at 10.1007/s11032-021-01264-7.
| S-EPMC10236124 | biostudies-literature