Population structure and genome-wide association studies in bread wheat for phosphorus efficiency traits using 35 K Wheat Breeder's Affymetrix array.
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ABSTRACT:
SUBMITTER: Soumya PR
PROVIDER: S-EPMC8027818 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Photosynthesis is the basis of plant growth and development, and is seriously affected by low phosphorus (P) stress. However, few studies have reported for the genetic foundation of photosynthetic response to low P stress in soybean. To address this issue, 219 soybean accessions were genotyped by 292,035 high-quality single nucleotide polymorphisms (SNPs) and phenotyped under normal and low P conditions in 2015 and 2016. These datasets were used to identify quantitative trait nucleotides (QTNs) for photosynthesis-related traits using mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA, and pKWmEB methods. As a result, 159 QTNs within 31 genomic regions were found to be associated with four photosynthesis-related traits under different P stress conditions. Among the 31 associated regions, five (q7-2, q8-1, q9, q13-1, and q20-2) were detected commonly under both normal and low P conditions, indicating the insensitivity of these candidate genes to low P stress; five were detected only under normal P condition, indicating the sensitivity of these candidate genes to low P stress; six were detected only under low P condition, indicating the tolerantness of these candidate genes to low P stress; 20 were reported in previous studies. Around the 159 QTNs, 52 candidate genes were mined. These results provide the important information for marker-assisted breeding in soybean and further reveal the basis for the application of P tolerance to photosynthetic capacity.
| S-EPMC6122521 | biostudies-literature
Project description:BackgroundWheat is a cool seasoned crop requiring low temperature during grain filling duration and therefore increased temperature causes significant yield reduction. A set of 125 spring wheat genotypes from International Maize and Wheat Improvement Centre (CIMMYT-Mexico) was evaluated for phenological and yield related traits at three locations in Pakistan under normal sowing time and late sowing time for expose to prolonged high temperature. With the help of genome-wide association study using genotyping-by-sequencing, marker trait associations (MTAs) were observed separately for the traits under normal and late sown conditions.ResultsSignificant reduction ranging from 9 to 74% was observed in all traits under high temperature. Especially 30, 25, 41 and 66% reduction was observed for days to heading (DH), plant height (PH), spikes per plant (SPP) and yield respectively. We identified 55,954 single nucleotide polymorphisms (SNPs) using genotyping by sequencing of these 125 hexaploid spring wheat genotypes and conducted genome-wide association studies (GWAS) for days to heading (DH), grain filled duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield per plot (GY). Genomic regions identified through GWAS explained up to 13% of the phenotypic variance, on average. A total of 139 marker-trait associations (MTAs) across three wheat genomes (56 on genome A, 55 on B and 28 on D) were identified for all the seven traits studied. For days to heading, 20; grain filled duration, 21; plant height, 23; spikes per plant, 13; grain numbers per spike, 8; thousand kernel weight, 21 and for grain yield, 33 MTAs were detected under normal and late sown conditions.ConclusionsThis study identifies the essential resource of genetics research and underpins the chromosomal regions of seven agronomic traits under normal and high temperature. Significant relationship was observed between the number of favored alleles and trait observations. Fourteen protein coding genes with their respective annotations have been searched with the sequence of seven MTAs which were identified in this study. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas.
| S-EPMC6475106 | biostudies-literature
Project description:Kernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP), and thousand-kernel weight (TKW), were evaluated in a panel consisting of 198 wheat accessions under six environments. Wheat accessions were genotyped using the 35K SNP iSelect chip array, resulting in a set of 13,228 polymorphic SNP markers that were used for genome-wide association study (GWAS). A total of 146 significant marker-trait associations (MTAs) were identified for five kernel traits on 21 chromosomes [–log10(P) ≥ 3], which explained 5.91–15.02% of the phenotypic variation. Of these, 12 stable MTAs were identified in multiple environments, and six superior alleles showed positive effects on KL, KP, and KDR. Four potential candidate genes underlying the associated SNP markers were predicted for encoding ML protein, F-box protein, ethylene-responsive transcription factor, and 1,4-α-glucan branching enzyme. These genes were strongly expressed in grain development at different growth stages. The results will provide new insights into the genetic basis of kernel traits in wheat. The associated SNP markers and predicted candidate genes will facilitate marker-assisted selection in wheat breeding.
| S-EPMC9207461 | biostudies-literature
Project description:Five genomic prediction models were applied to three wheat agronomic traits-grain yield, heading date and grain test weight-in three breeding populations, each comprising about 350 doubled haploid or recombinant inbred lines evaluated in three locations during a 3-year period. The prediction accuracy, measured as the correlation between genomic estimated breeding value and observed trait, was in the range of previously published values for yield (r = 0.2-0.5), a trait with relatively low heritability. Accuracies for heading date and test weight, with relatively high heritabilities, were about 0.70. There was no improvement of prediction accuracy when two or three breeding populations were merged into one for a larger training set (e.g., for yield r ranged between 0.11 and 0.40 in the respective populations and between 0.18 and 0.35 in the merged populations). Cross-population prediction, when one population was used as the training population set and another population was used as the validation set, resulted in no prediction accuracy. This lack of cross-population prediction accuracy cannot be explained by a lower level of relatedness between populations, as measured by a shared SNP similarity, since it was only slightly lower between than within populations. Simulation studies confirm that cross-prediction accuracy decreases as the proportion of shared QTLs decreases, which can be expected from a higher level of QTL × environment interactions.
| S-EPMC4544631 | biostudies-literature
Project description:ERECTA encodes a receptor-like kinase and is proposed as a candidate for determining transpiration efficiency of plants. Two genes homologous to ERECTA in Arabidopsis were identified on chromosomes 6 (TaER2) and 7 (TaER1) of bread wheat (Triticum aestivum L.), with copies of each gene on the A, B and D genomes of wheat. Similar expression patterns were observed for TaER1 and TaER2 with relatively higher expression of TaER1 in flag leaves of wheat at heading (Z55) and grain-filling (Z73) stages. Significant variations were found in the expression levels of both TaER1 and TaER2 in the flag leaves at both growth stages among 48 diverse bread wheat varieties. Based on the expression of TaER1 and TaER2, the 48 wheat varieties could be classified into three groups having high (5 varieties), medium (27 varieties) and low (16 varieties) levels of TaER expression. Significant differences were also observed between the three groups varying for TaER expression for several transpiration efficiency (TE)- related traits, including stomatal density (SD), transpiration rate, photosynthetic rate (A), instant water use efficiency (WUEi) and carbon isotope discrimination (CID), and yield traits of biomass production plant-1 (BYPP) and grain yield plant-1 (GYPP). Correlation analysis revealed that the expression of TaER1 and TaER2 at the two growth stages was significantly and negatively associated with SD (P<0.01), transpiration rate (P<0.05) and CID (P<0.01), while significantly and positively correlated with flag leaf area (FLA, P<0.01), A (P<0.05), WUEi (P<0.05), BYPP (P<0.01) and GYPP (P<0.01), with stronger correlations for TaER1 than TaER2 and at grain-filling stage than at heading stage. These combined results suggested that TaER involved in development of transpiration efficiency -related traits and yield in bread wheat, implying a function for TaER in regulating leaf development of bread wheat and contributing to expression of these traits. Moreover, the results indicate that TaER could be exploitable for manipulating important agronomical traits in wheat improvement.
| S-EPMC4457575 | biostudies-literature
Project description:Potassium use efficiency, a complex trait, directly impacts the yield potential of crop plants. Low potassium efficiency leads to a high use of fertilizers, which is not only farmer unfriendly but also deteriorates the environment. Genome-wide association studies (GWAS) are widely used to dissect complex traits. However, most studies use single-locus one-dimensional GWAS models which do not provide true information about complex traits that are controlled by multiple loci. Here, both single-locus GWAS (MLM) and multi-locus GWAS (pLARmEB, FASTmrMLM, mrMLM, FASTmrEMMA) models were used with genotyping from 90 K Infinium SNP array and phenotype derived from four normal and potassium-stress environments, which identified 534 significant marker-trait associations (MTA) for agronomic and potassium related traits: pLARmEB = 279, FASTmrMLM = 213, mrMLM = 35, MLM = 6, FASTmrEMMA = 1. Further screening of these MTA led to the detection of eleven stable loci: q1A, q1D, q2B-1, q2B-2, q2D, q4D, q5B-1, q5B-2, q5B-3, q6D, and q7A. Moreover, Meta-QTL (MQTL) analysis of four independent QTL studies for potassium deficiency in bread wheat located 16 MQTL on 13 chromosomes. One locus identified in this study (q5B-1) colocalized with an MQTL (MQTL_11 ), while the other ten loci were novel associations. Gene ontology of these loci identified 20 putative candidate genes encoding functional proteins involved in key pathways related to stress tolerance, sugar metabolism, and nutrient transport. These findings provide potential targets for breeding potassium stress resistant wheat cultivars and advocate the advantages of multi-locus GWAS models for studying complex traits.
| S-EPMC7041172 | biostudies-literature
Project description:Phosphorus (P) efficiency (PE), which comprises phosphorus uptake (PupE) and utilization efficiency (PutE), is considered as one of the most important factors for crop yield. In the present study, 11 seedling traits and 13 maturity traits related to wheat PE and morphology were investigated using a set of recombinant inbred lines (RILs) derived from the cross of "TN 18 × LM 6," under hydroponic culture trials and field trials at low P (LP) and normal P (NP) levels in two different years, respectively. The LP input reduced of biomass, yield and PupE traits, but increased PutE traits. A total of 163 QTLs for seedling and maturity traits under different P levels and their AV, and 15 QTLs for relative traits were detected on 21 chromosomes. Of these, 49 and 63 QTLs for were detected specially in LP and NP treatments, respectively. We found 11 relatively high-frequency QTLs (RHF-QTLs) and four important QTL clusters, which may be the potential targets for marker-assisted selection (MAS) in wheat breeding programs for PE. Favorable relationships for breeding programs were found in the four important QTL clusters, which allow the possibility of improving the morphological traits and PutE simultaneously. A total of 29 markers which associated with 51 QTLs were found highly homologous with EST sequences, which suggested that they were potential functional loci. We suggested that the four biomass traits (SDW, RDW, TDW, and RSDW), five yield traits (SN, PH, TGW, GWP, and StWP) and two relative traits (Rstwp and Rgwp) can be considered as the primary indexes for the evaluation of PE for they are easy to identify on a large-scale.
| S-EPMC5402226 | biostudies-literature
Project description:BackgroundNatural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55 K Affymetrix GeneChip Wheat Genome Array, which is a 3' in vitro transcription (3'IVT) expression array. We selected five different tissue types for assay to enable maximum discovery, and used the 'Chinese Spring' wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3'IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept.ResultsBy using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. Quality assurance verified that successful hybridization did occur in the antisense-strand assay. A stringent threshold for positive hybridization was applied, which resulted in the identification of 110 sense-antisense transcript pairs, as well as 80 potentially antisense-specific transcripts. Strand-specific RT-PCR validated the microarray observations, and showed that antisense transcription is likely to be tissue specific. For the annotated sense-antisense transcript pairs, analysis of the gene ontology terms showed a significant over-representation of transcripts involved in energy production. These included several representations of ATP synthase, photosystem proteins and RUBISCO, which indicated that photosynthesis is likely to be regulated by antisense transcripts.ConclusionThis study demonstrated the novel use of an adapted labeling protocol and a 3'IVT GeneChip array for large-scale identification of antisense transcription in wheat. The results show that antisense transcription is relatively abundant in wheat, and may affect the expression of valuable agronomic phenotypes. Future work should select potentially interesting transcript pairs for further functional characterization to determine biological activity.
| S-EPMC2694213 | biostudies-literature
Project description:The root system architectures (RSAs) largely decide the phosphorus use efficiency (PUE) of plants by influencing the phosphorus uptake. Very limited information is available on wheat's RSAs and their deciding factors affecting phosphorus uptake efficiency (PupE) due to difficulties in adopting scoring values used for evaluating root traits. Based on our earlier research experience on nitrogen uptake efficiency screening under, hydroponics and soil-filled pot conditions, a comprehensive study on 182 Indian bread wheat genotypes was carried out under hydroponics with limited P (LP) and non-limiting P (NLP) conditions. The findings revealed a significant genetic variation, root traits correlation, and moderate to high heritability for RSAs traits namely primary root length (PRL), total root length (TRL), total root surface area (TSA), root average diameter (RAD), total root volume (TRV), total root tips (TRT) and total root forks (TRF). In LP, the expressions of TRL, TRV, TSA, TRT and TRF were enhanced while PRL and RAD were diminished. An almost similar pattern of correlations among the RSAs was also observed in both conditions except for RAD. RAD exhibited significant negative correlations with PRL, TRL, TSA, TRT and TRF under LP (r = -0.45, r = -0.35, r = -0.16, r = -0.30, and r = -0.28 respectively). The subclass of TRL, TSA, TRV and TRT representing the 0-0.5 mm diameter had a higher root distribution percentage in LP than NLP. Comparatively wide range of H' value i.e. 0.43 to 0.97 in LP than NLP indicates that expression pattern of these traits are highly influenced by the level of P. In which, RAD (0.43) expression was reduced in LP, and expressions of TRF (0.91) and TSA (0.97) were significantly enhanced. The principal component analysis for grouping of traits and genotypes over LP and NLP revealed a high PC1 score indicating the presence of non-crossover interactions. Based on the comprehensive P response index value (CPRI value), the top five highly P efficient wheat genotypes namely BW 181, BW 103, BW 104, BW 143 and BW 66, were identified. Considering the future need for developing resource-efficient wheat varieties, these genotypes would serve as valuable genetic sources for improving P efficiency in wheat cultivars. This set of genotypes would also help in understanding the genetic architecture of a complex trait like P use efficiency.
| S-EPMC8486105 | biostudies-literature
Project description:BackgroundA large number of natural antisense transcripts have been identified in human and mouse genomes. Study of their potential functions clearly requires cost-efficient method for expression analysis.ResultsHere we show that Affymetrix Exon arrays, which were designed to detect conventional transcripts in the sense orientation, can be used to monitor antisense expression across all exonic loci in mammalian genomes. Through modification of the cDNA synthesis protocol, we labeled single-strand cDNA in the reverse orientation as in the standard protocol, thus enabling the detection of antisense transcripts using the same array. Applying this technique to human Jurkat cells, we identified antisense transcription at 2,088 exonic loci of 1,516 UniGene clusters. Many of these antisense transcripts were not observed previously and some were validated by orientation-specific RT-PCR.ConclusionOur results suggest that with a modified protocol Affymetrix human, mouse and rat Exon arrays can be used as a routine method for genome-wide analysis of antisense transcription in these genomes.
| S-EPMC2257944 | biostudies-literature