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Molecular Marker Technology for Crop Improvement

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Nguyễn Gia Hào

Academic year: 2023

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Genetic dissection of seminal root system architecture in Mediterranean durum wheat soils from the Genome Wide Association Study. Genetic dissection of seed root system architecture in Mediterranean durum wheat soils from the Genome Wide Association Study.Agronomy.

Genetic Dissection of the Seminal Root System Architecture in Mediterranean Durum Wheat

  • Introduction
  • Materials and Methods 1. Plant Material
  • Results
  • Discussion
  • Conclusions

Of the 176 markers showing significant associations, 31 were identified in the reference sequence of the wheat genome [34] (Table 5). The comparison of the genome regions identified in the present study with those related to yield and yield components by Roselló et al.

Figure 1. Experimental setup for root system architecture analysis. First, seeds were placed on humid filter paper (1) and rolled
Figure 1. Experimental setup for root system architecture analysis. First, seeds were placed on humid filter paper (1) and rolled

SSR Marker-Assisted Management of Parental Germplasm in Sugarcane (Saccharum spp. hybrids)

Materials and Methods 1. Plant Materials

The K value was used to estimate the number of clusters of the clones based on the genotypic data. In this study, we used 21 pairs of SSR primers to investigate the genetic diversity and population structure of 150 of the most commonly used parental clones.

Table 1. The 150 sugarcane accessions used in the experiment.
Table 1. The 150 sugarcane accessions used in the experiment.

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the

Materials and Methods

Interestingly, KASP genotyping results revealed that all indigenous avocado accessions included in this study are Guatemalan × West Indian hybrids. In addition, cluster analysis grouped two indigenous avocado specimens from Yunnan Province with indigenous avocado specimens from Guangxi Province.

Figure 1. Length distribution of 651,260 reads of insert in avocadomesocarp.
Figure 1. Length distribution of 651,260 reads of insert in avocadomesocarp.

Assessment of Genetic Diversity in Differently Colored Raspberry Cultivars Using SSR Markers

Nine SSR markers (six based on Rubus and three on Fragaria nucleotide sequences of the flavonoid biosynthesis genes) were used to estimate genetic diversity in 19 raspberry (R. idaeus) and two black raspberry (R. occidentalis) cultivars. A UPGMA dendrogram was constructed for 21 raspberry cultivars based on seven SSR markers located in the flavonoid biosynthesis genes (Figure 1). In this study, we report on the evaluation of a number of red and black raspberry cultivars using SSR loci representing known sequences of flavonoid biosynthesis pathway genes, which synthesize biologically active substances with high antioxidant activity - flavonols and anthocyanins.

Of these microsatellite loci, six (RcFH01, FaFS01, FaFS02, RiAS01, FaAR01 and RhUF01) were located in the structural genes of flavonoid biosynthesis (F3H, FLS, ANS, ANR and UFGT) and two (RiMY01 and RiTT01) in the regulatory genes. (MYB10 and TTG1). Cluster analysis of the SSR markers located in the flavonoid biosynthesis genes showed a clear separation between the black raspberry (R. occidentalis) cultivars with black colored berries and the red raspberry (R. idaeus) cultivars with berries that from yellow to dark colored are red (figure 1). Transcriptional control of flavonoid biosynthesis: fine tuning of the MYB-bHLH-WD40 (MBW) complex. Plant signal.

Table 1. Parentage and fruit color of the Rubus cultivars used in the study.
Table 1. Parentage and fruit color of the Rubus cultivars used in the study.

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Maize with

Materials and Methods 1. Trial Conditions and Phenotyping

The extent of LD was estimated using the correlation coefficients of the allelic frequencies (r2) taking into account all the possible combinations of the alleles. This method considers the 95% confidence intervals of the disequilibrium coefficient (D') values ​​and builds a haplotype block whose LD is classified as a “strong LD” type (Higher than 0.98 and lower interval limit of >0.7). The HB- and SNP-based association analyzes were performed using a mixed linear model (MLM) in TASSEL 3.0 and TASSEL 5.2, respectively [24], which takes into account the effects of population structure (Q) and genetic relationships or matrix consanguinity (K) ) among inbred lines.

The adjusted input means of the general linear model (experimental design) were used as the adjusted phenotypes according to Contreras-Soto et al. To this end, a window (or threshold) of twice the distance indicated by the LD analysis was established, with the marker in the placed in the center of the window. The gene prioritization was performed using MaizeNet [12] based on the connections of the candidate genes to the genes in one estimated network with previously associated genes with flowering time in Zea mays.

Results and Discussion 1. Genetic Structure

An average of approximately 20,000 SNPs per chromosome met the 95% confidence interval criteria proposed by Gabriel et al. Analysis of the LD pattern allowed the identification and characterization of several HBs (or strongly linked genomic regions) because there is strong LD between the SNPs that make it up. On the other hand, 64 QTLs associated with flowering time in maize were identified by Liu et al.

Consistent with this, the significant HB and all SNP associations explained no more than 10% of the total variation. Twenty-five of the 45 SNPs detected by GWAS (ie, 56%) were found to be part of a haplotype block, which in turn was significantly associated with a given trait. Based on the physical position of the maize reference genome (http://www.maizegdb.org//), 51 candidate genes were identified next to the significant SNPs and HBs (Table S1), of which 11 were present in more than one trait (FF and MF) (Table S1).

Table 1. Summary of information on linkage disequilibrium (LD) and haplotype blocks (HBs) determined in inbred lines of tropical maize
Table 1. Summary of information on linkage disequilibrium (LD) and haplotype blocks (HBs) determined in inbred lines of tropical maize

Conclusions

-functional networks assessed using genes identified by SNP and haplotype-based GWAS (A, B), genes identified by network-based gene prioritization (in MaizeNet) for flowering time and subnetworks enriched with Gene Ontology annotations related to biological female flowering (FF) processes in MaizeNet. Identification of genetic variants associated with flowering time in maize using an extremely large multigenetic background population. A plant. Genetic architecture of flowering time and photoperiod sensitivity in maize as revealed by QTL screening and meta-analysis. J.

Quantitative genetic analysis of flowering time, leaf number and photoperiod sensitivity in maize (Zea maysL.).J. Genetic architecture of flowering time in maize as inferred from meta-analysis of quantitative trait loci and conservation of synteny with the rice genome. Genetics. Molecular and functional characterization of PEBP genes in barley reveals diversification of their roles in flowering. A plant.

Identification and Verification of Quantitative Trait Loci Affecting Milling Yield of Rice

In the present study, QTL analysis was used to determine the dependence of milled and heading rice yield on milling quality and grain yield. Descriptive statistics of the seven traits in the three RIL populations are presented in Table S1. Markers within the blue rectangle are flanking markers of QTLs detected in the TI population.

The other six QTL regions found in the Ti52-3 population were not detected in the TI population. In the neighboring region RM6-RM240, QTLs for the same four traits were detected in the TI population. In the GW5-Chalk5 region, QTLs with large effects for MR were detected in the TI and XM populations.

Table 1. Simple correlation coefficients between seven traits in three RIL populations of rice.
Table 1. Simple correlation coefficients between seven traits in three RIL populations of rice.

An SNP-Based High-Density Genetic Linkage Map for Tetraploid Potato Using Specific Length Amplified

The HighMap software was used to construct a high-density genetic linkage map of tetraploid potato [ 34 ]. Heatmaps were also constructed to evaluate the quality of the genetic map using pairwise recombination values ​​for the 3001 SNP markers (FigureA3). To our knowledge, only one high-density SNP genetic linkage map has been reported for tetraploid potatoes due to the high heterozygosity of autotetraploid potato [ 20 ].

The integrated high genetic linkage map generated here has the best coverage of the potato genome and the closest marker density reported for tetraploid potato to date. High-density genetic map construction and mapping of the homologous transformation sterility (hts) gene in wheat using gbsmarkers. Construction of the first high-density genetic linkage map of salvia miltiorrhiza using specific length amplified fragment (SLAF) sequencing. Sci.

Table 1. Basic statistic of the SLAF-seq data in tetraploid potato.
Table 1. Basic statistic of the SLAF-seq data in tetraploid potato.

Mapping Agronomic and Quality Traits in Elite Durum Wheat Lines under Differing Water Regimes

Material and Methods

SV: sedimentation volume; SDS: sedimentation index; and GPC: wheat protein content; Figure S5: Quantile quantile plots from GWAS analysis for durum wheat SNP markers (mapped and unmapped). SV: sedimentation volume; SDS: sedimentation index; and GPC: wheat protein content; Figure S6: Blue copper protein gene cluster on durum wheat chromosome 1B. Map positions of molecular markers are shown in both the durum wheat genome [ 71 ] and the RefSeqv1 wheat reference assembly [ 69 ]; Supplementary material S1.

Genotype x environment interaction for quality traits in cultivars of durum wheat adapted to different environments.Afr. Genome-wide association and prediction of grain and semolina quality traits in durum wheat breeding populations.Plant Genome2017,10. Mapping of QTL for agronomic traits and core traits in durum wheat (Triticum durumDesf.). Euphytica.

Table 1. Agronomic and quality assessment of wheat field trials. The number of lines, year, location and water regime applied is shown.
Table 1. Agronomic and quality assessment of wheat field trials. The number of lines, year, location and water regime applied is shown.

Exploring the Genetic Architecture of Root-Related Traits in Mediterranean Bread Wheat Landraces by

The results of the GWAS for root-related properties are reported in Figure 3 and Supplementary Materials, Table S2. The results of the GWAS for GY are reported in Figure 3 and Supplementary Materials, Table S3. The broad morphological plasticity of the root system to different soil conditions and the role of root characteristics in arid environments are well known [34,35].

The present study evaluated root-related traits in a collection of Mediterranean bread wheat landraces, representative of the variability existing for the species in the Mediterranean basin [23]. The complexity of genetic control of root traits was confirmed with 135 marker-trait associations identified in the present study. The role of the F-box gene TaFBA1 from wheat (Triticum aestivumL.) in drought tolerance.Plant Physiol.

Figure 1. Experimental setup for the analysis of seminal root traits. Seeds were placed 8 cm apart on moist filter paper (A) and kept in a box with distilled water in a growth chamber for 14 days at 22 ◦ C under a 16-h light photoperiod (B)
Figure 1. Experimental setup for the analysis of seminal root traits. Seeds were placed 8 cm apart on moist filter paper (A) and kept in a box with distilled water in a growth chamber for 14 days at 22 ◦ C under a 16-h light photoperiod (B)

Improvement of a RD6 Rice Variety for Blast Resistance and Salt Tolerance through

Marker-Assisted Backcrossing

Evaluation of salt tolerance and shock resistance evaluation in BC4F3 populations (Experiment 3) Evaluation of salt tolerance of BC4F3 lines was carried out in greenhouses at the Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand. Eight of the BC2F2:3 lines were evaluated for salt tolerance at the seedling stage using saline and artificial soil salinity methods. The results showed that the Saltol QTL in the BC4F3 population showed better results in salt tolerance than the recurrent parent (RD6).

The BC4F3132-12 maintained agronomic traits similar to those of the recurrent parent (RD6) for nine traits, except for the 1000/SW (1000 seed weight), in which the RD6 presented moderate susceptibility (MS) to leaf and neck blast, which resulted in low grain filling (Table 4). Consequently, the performance of the RD6 introgression lines was similar to that of the original RD6 variety (Table4, Figure2). Improvement of the RD6 rice variety for salt tolerance and blast resistance was successfully achieved using the SaltolQTL andqBl(1,2,11, en12) through marker-assisted backcrossing, along with phenotypic selection.

Figure 1. Breeding schematics for the development and validation of the RD6 NILs populations.
Figure 1. Breeding schematics for the development and validation of the RD6 NILs populations.

Identification of QTLs Controlling

Materials and Methods 1. Germplasm and Phenotyping

The statistical significance of QTL was assessed using permutation tests (1000 replications) for all traits. Broad sense heritability estimates of the traits derived from the variance components ranged from 0.47 for Strigaskade to 0.70 for ears per plant. Similarly, qgy-2.1 and qsd-2 were detected for grain yield and the number of emerged Striga plants consistently identified in the same position at each of the two locations.

The normal distribution observed for grain yield and Strigas damage in this study is a result of the very different genotypes that differ in the mapping population [64]. The selection of parental lines with varying levels of resistance to Striga allowed sufficient separation of the traits in the population. Putative candidate genes associated with some of the identified QTLs for Stria resistance indicator traits are presented in Table 4.

Figure 1. Box plots showing the distribution of (A) grain yield (YIELD, t/ha), (B) emerged Striga plants (ESP), (C) Striga damage rating (SDR) and (D) number of ears per plant (EPP) under artificial Striga infestation at Mokwa (MK) and Abuja (AB) in 2018
Figure 1. Box plots showing the distribution of (A) grain yield (YIELD, t/ha), (B) emerged Striga plants (ESP), (C) Striga damage rating (SDR) and (D) number of ears per plant (EPP) under artificial Striga infestation at Mokwa (MK) and Abuja (AB) in 2018

Molecular Assisted Selection for Pollination-Constant and Non-Astringent Type without Male Flowers in

Results and Discussion

The capacity to develop male flowers was clearly indicated by the presence of the amplified band (320 bp). Figure 2a shows the results on an agarose gel of the presence of male flowers in the genotypes 'Agakaki', 'Cal Fuyu' and the selection 'F-1.34 from the IVIA breeding program. Total correlation between the phenotype and the presence/absence of the band was obtained for all the genotypes studied (Table 1).

This production of acetaldehyde resulted in discoloration of the flesh around the seeds, which interferes with postharvest treatment to remove pungency in the fruit [25]. In breeding programs involving non-astringent varieties, discrimination of the presence of male flowers is also necessary. Markers DlSx-AF4, associated with male flower production and AST associated with fruit astringency, have been validated in a date palm germplasm collection.

Figure 3. Three types of astringent persimmon according to the amount of acetaldehyde produced by the seed; (A) fruits of pollination constant astringent (PCA), PVA and pollination variant non-astringent (PVNA; from right to left) and (B) distribution of c
Figure 3. Three types of astringent persimmon according to the amount of acetaldehyde produced by the seed; (A) fruits of pollination constant astringent (PCA), PVA and pollination variant non-astringent (PVNA; from right to left) and (B) distribution of c

Hình ảnh

Figure 3. Summary of marker trait associations (MTA). (A) Number of MTAs per chromosome.
Figure 4. MTA-QTL map. MTA-QTLs are indicated in bold on the left side of the chromosome and traits involved in each MTA-QTL are on the right side
Table 3. Cont.
Table 1. The 150 sugarcane accessions used in the experiment.
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