Identification and validation of QTL and their associated genes for pre-emergent metribuzin tolerance in hexaploid wheat (Triticum aestivum L.)

Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat

The current study focuses on identifying the candidate genes of a grain yield QTL from a double haploid population, Westonia × Kauz. The QTL region spans 20 Mbp on the IWGSC whole-genome sequence flank with 90K SNP markers. The IWGSC gene annotation revealed 16 high-confidence genes and 41 low-confidence genes. Bioinformatic approaches, including functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available gene expression data, enabled the short-listing of four genes for further confirmation. Complete sequencing of those four genes demonstrated that only two genes are polymorphic between the parental cultivars, which are the ferredoxin-like protein gene and the tetratricopeptide-repeat (TPR) protein gene. The two genes were selected for downstream investigation. Two SNP variations were observed in the exon for both genes, with one SNP resulting in changes in amino acid sequence. qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines along with the parental cultivar Westonia. In contrast, their expression was significantly lower in the low-yielding lines in the other parent. It can be concluded that these two genes are the contributing genes to the grain yield QTL.

Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat

BACKGROUND

Weeds reduce wheat yields in dryland farming systems. Herbicides such as metribuzin are commonly used to control weeds. However, wheat has a narrow safety margin against metribuzin. Standing crops such as wheat with weeds in the same field can also be killed by the same dose of metribuzin. Therefore, it is important to identify metribuzin resistance genes and understand the resistance mechanism in wheat for sustainable crop production. A previous study identified a significant metribuzin resistance wheat QTL, Qsns.uwa.4 A.2, explaining 69% of the phenotypic variance for metribuzin resistance.

RESULTS

Two NIL pairs with the most contrasting performance in the metribuzin treatment and different in genetic backgrounds were compared using RNA sequence analysis, identifying nine candidate genes underlying Qsns.uwa.4 A.2 responsible for metribuzin resistance. Quantitative RT-qPCR further validated the candidate genes, with TraesCS4A03G1099000 (nitrate excretion transporter), TraesCS4A03G1181300 (aspartyl protease), and TraesCS4A03G0741300 (glycine-rich proteins) identified as key factors for metribuzin resistance.

CONCLUSION

Identified markers and key candidate genes can be used for selecting metribuzin resistance in wheat.

Chromosome groups 5, 6 and 7 harbor major quantitative trait loci controlling root traits in bread wheat (Triticum aestivum L.)

Identifying genomic regions for root traits in bread wheat can help breeders develop climate-resilient and high-yielding wheat varieties with desirable root traits. This study used the recombinant inbred line (RIL) population of Synthetic W7984 × Opata M85 to identify quantitative trait loci (QTL) for different root traits such as rooting depth (RD), root dry mass (RM), total root length (RL), root diameter (Rdia) and root surface areas (RSA1 for coarse roots and RSA2 for fine roots) under controlled conditions in a semi-hydroponic system. We detected 14 QTL for eight root traits on nine wheat chromosomes; we discovered three QTL each for RD and RSA1, two QTL each for RM and RSA2, and one QTL each for RL, Rdia, specific root length and nodal root number per plant. The detected QTL were concentrated on chromosome groups 5, 6 and 7. The QTL for shallow RD (Q.rd.uwa.7BL: Xbarc50) and high RM (Q.rm.uwa.6AS: Xgwm334) were validated in two independent F₂ populations of Synthetic W7984 × Chara and Opata M85 × Cascade, respectively. Genotypes containing negative alleles for Q.rd.uwa.7BL had 52% shallower RD than other Synthetic W7984 × Chara population lines. Genotypes with the positive alleles for Q.rm.uwa.6AS had 31.58% higher RM than other Opata M85 × Cascade population lines. Further, we identified 21 putative candidate genes for RD (Q.rd.uwa.7BL) and 13 for RM (Q.rm.uwa.6AS); TraesCS6A01G020400, TraesCS6A01G024400 and TraesCS6A01G021000 identified from Q.rm.uwa.6AS, and TraesCS7B01G404000, TraesCS7B01G254900 and TraesCS7B01G446200 identified from Q.rd.uwa.7BL encoded important proteins for root traits. We found germin-like protein encoding genes in both Q.rd.uwa.7BL and Q.rm.uwa.6AS regions. These genes may play an important role in RM and RD improvement. The identified QTL, especially the validated QTL and putative candidate genes are valuable genetic resources for future root trait improvement in wheat.

Fruit Morphology and Ripening-Related QTLs in a Newly Developed Introgression Line Collection of the Elite Varieties 'Védrantais' and 'Piel de Sapo'

Melon is an economically important crop with widely diverse fruit morphology and ripening characteristics. Its diploid sequenced genome and multiple genomic tools make this species suitable to study the genetic architecture of fruit traits. With the development of this introgression line population of the elite varieties 'Piel de Sapo' and 'Védrantais', we present a powerful tool to study fruit morphology and ripening traits that can also facilitate characterization or pyramidation of QTLs in inodorous melon types. The population consists of 36 lines covering almost 98% of the melon genome, with an average of three introgressions per chromosome and segregating for multiple fruit traits: morphology, ripening and quality. High variability in fruit morphology was found within the population, with 24 QTLs affecting six different traits, confirming previously reported QTLs and two newly detected QTLs, FLQW5.1 and FWQW7.1. We detected 20 QTLs affecting fruit ripening traits, six of them reported for the first time, two affecting the timing of yellowing of the rind (EYELLQW1.1 and EYELLQW8.1) and four at the end of chromosome 8 affecting aroma, abscission and harvest date (EAROQW8.3, EALFQW8.3, ABSQW8.3 and HARQW8.3). We also confirmed the location of several QTLs, such as fruit-quality-related QTLs affecting rind and flesh appearance and flesh firmness.

Genomic Regions, Molecular Markers, and Flanking Genes of Metribuzin Tolerance in Wheat (Triticum aestivum L.)

Understanding the genetics of metribuzin (a group C herbicide) tolerance in wheat is vital in developing tolerant cultivars to improve wheat productivity in dryland farming systems. This study investigated metribuzin tolerance in wheat by conducting a Genome-wide Association Studies (GWAS) with a panel of 150 wheat genotypes of diverse genetic backgrounds and genotyped them with the wheat 90 K SNP genotyping assay. The phenotyping was conducted in a temperature-controlled glasshouse at the University of Western Australia (UWA). Genotypes were sprayed with a metribuzin dose of 400 grams of active ingredient (g. a.i.) ha^-1 as pre-emergent in a specialized spraying cabinet and transferred to the glasshouse where the tolerance level of the genotypes was assessed by measuring the relative reduction in chlorophyll content of the leaves. The decrease in chlorophyll content of the treated plants compared to the control was regarded as the phytotoxic effects of metribuzin. GWAS analysis following a mixed linear model revealed 19 genomic regions with significant marker-trait associations (MTAs), including ten on chromosome 6A, three on chromosome 2B, and one on chromosomes 3A, 5B, 6B 6D, 7A, and 7B, respectively. Sequences of the significant markers were blasted against the wheat genome, IWGSC RefSeq V1.0, and candidate genes having annotations related to herbicide tolerance in wheat, especially in pathways reported to be involved in metribuzin tolerance, such as cytochrome P450 pathways and ATP Binding Cassette (ABC) superfamilies, were identified in these genomic regions. These included TraesCS6A01G028800, TraesCS6A02G353700, TraesCS6A01G326200, TraesCS7A02G331000, and TraesCS2B01G465200. These genomic regions were validated on 30 top tolerant and 30 most susceptible genotypes using the five closest SSR makers to the flanked SNPs. Sufficient polymorphism was detected on two markers (wms193 and barc1036) that were found to differentiate between the susceptible and tolerant alleles and a t-test analysis of the phenotypic data shows a significant (value of p < 0.001) difference suggesting that these markers can be used for marker-assisted selection (MAS) in metribuzin studies and wheat breeding programs.

Identification and Validation of a Chromosome 4D Quantitative Trait Locus Hotspot Conferring Heat Tolerance in Common Wheat (Triticum aestivum L.)

Understanding of the genetic mechanism of heat tolerance (HT) can accelerate and improve wheat breeding in dealing with a warming climate. This study identified and validated quantitative trait loci (QTL) responsible for HT in common wheat. The International Triticeae Mapping Initiative (ITMI) population, recombinant inbreed lines (RILs) derived from a cross between Synthetic W7984 and Opata M85, was phenotyped for shoot length, root length, whole plant length under heat stress and corresponding damage indices (DIs) to compare HT performances of individuals. Wide variations among the RILs were shown for all the traits. A total of 13 QTL including 9 major QTL and 4 minor QTL were identified, distributed on 6 wheat chromosomes. The six major QTL with the highest R² were associated with different traits under heat stress. They were all from Opata M85 background and located within a 2.2 cm interval on chromosome 4D, making up a QTL hotspot conferring HT in common wheat. The QTL hotspot was validated by genotyping-phenotyping association analysis using single-nucleotide-polymorphism (SNP) assays. The QTL, especially the 4D QTL hotspot identified and validated in this study, are valuable for the further fine mapping and identification of key genes and exploring genetic mechanism of HT in wheat.

Effects of Metribuzin Herbicide on Some Morpho-Physiological Characteristics of Two Echinacea Species

Echinacea is a perennial plant that is used for its phytotherapeutic potential. Echinacea crops are often affected by invasive weeds. One of the most effective strategies in weed control is the use of chemicals such as herbicides. However, herbicides also affect the physiological and morphological processes of Echinacea. For this reason, the aim of this study was to determine the effects of different dosages (0, 250, 500, 750, 1000, and 1250 g ha−1) of the postemergent herbicide metribuzin on some morphological and physiological characteristics of Echinacea purpurea and Echinacea angustifolia collected from different locations in Iran (E. purpurea from the Shiraz and Isfahan regions and E. angustifolia from the Ardestan and Kazerun regions). Application of metribuzin decreased leaf dry weight for both Echinacea species at high doses (750 and 1250 g ha−1). At high metribuzin dose (1250 g ha−1), E. purpurea Shiraz leaves showed an increase in MDA (malondialdehyde) up to 9.14, while in other species the MDA content was lower. Minimum and maximum fluorescence increased at both the registered dosage (500 g ha−1) and at high doses (750–1250 g ha−1) of metribuzin treatments in both species. The Fv/Fm (maximum quantum yield) value was reduced in herbicide treated species, compared to the control, starting at the 250 g ha−1 dose, and was lowest at 750 g ha−1 dose. The results of this study indicate that metribuzin has adverse effects on the physiology and morphology of Echinacea species at dosages above 500 g ha−1.

Characterisation of a 4A QTL for Metribuzin Resistance in Wheat by Developing Near-Isogenic Lines

Wheat (Triticum aestivum L.) production is constantly affected by weeds in the farming system. Chemical-based weed management is widely practiced; broad-spectrum herbicides such as metribuzin have been successfully used to control weeds in Australia and elsewhere of the world. Breeding metribuzin-resistant wheat through genetic improvement is needed for effective control of weeds. Quantitative trait loci (QTLs) mapping efforts identified a major QTL on wheat chromosome 4A, explaining up to 20% of the phenotypic variance for metribuzin resistance. The quantitative nature of inheritance of this QTL signifies the importance of near-isogenic lines (NILs), which can convert a quantitative trait into a Mendelian factor for better resolution of the QTL. In the current study, NILs were developed using a heterogeneous inbred family method combined with a fast generation-cycling system in a population of Chuan Mai 25 (resistant) and Ritchie (susceptible). Seven pairs of NILs targeting the 4A QTL for metribuzin resistance were confirmed with a molecular marker and phenotyping. The resistant allele from the resistant parent increased metribuzin resistance by 63-85% (average 69%) compared with the susceptible allele from the susceptible parent. Segregation analysis in the NIL pairs for thousand grain weight (TGW) (g), biomass per plant (kg), tillers per plant, plant height (cm), yield per plant, and powdery mildew visual score (0-9) indicated that these traits were linked with metribuzin resistance. Similarly, TGW was observed to co-segregate with metribuzin resistance in most confirmed NILs, signifying that the two traits are controlled by closely linked genes. The most contrasting NILs can be further characterised by transcriptomic and proteomic analyses to identify the candidate genes responsible for metribuzin resistance.

Using chlorate as an analogue to nitrate to identify candidate genes for nitrogen use efficiency in barley

Nitrogen (N) is one of the most important macronutrients for crop growth and development. Large amounts of N fertilizers are applied exogenously to improve grain yield and quality, which has led to environmental pollution and high cost of production. Therefore, improvement of N use efficiency (NUE) is a very important aspect for sustainable agriculture. Here, a pilot experiment was firstly conducted with a set of barley genotypes with confirmed NUE to validate the fast NUE screening, using chlorate as an analogue to nitrate. High NUE genotypes were susceptible to chlorate-induced toxicity whereas the low NUE genotypes were tolerant. A total of 180 barley RILs derived from four parents (Compass, GrangeR, Lockyer and La Trobe) were further screened for NUE. Leaf chlorosis induced by chlorate toxicity was the key parameter observed which was later related to low-N tolerance of the RILs. There was a distinct variation in chlorate susceptibility of the RILs with leaf chlorosis in the oldest leaf ranging from 10 to 80%. A genome-wide association study (GWAS) identified 9 significant marker-trait associations (MTAs) conferring high chlorate sensitivity on chromosomes 2H (2), 3H (1), 4H (4), 5H (1) and Un (1). Genes flanking with these markers were retrieved as potential targets for genetic improvement of NUE. Genes encoding Ferredoxin 3, leucine-rich receptor-like protein kinase family protein and receptor kinase are responsive to N stress. MTA4H5468 which exhibits concordance with high NUE phenotype can further be explored under different genetic backgrounds and successfully applied in marker-assisted selection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01239-8.

Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.)

Weeds are the biggest threat to cropping system sustainability in wheat. Metribuzin is a versatile herbicide for broad-spectrum weed management. Understanding key genes, mechanisms and functional markers are essential to develop higher metribuzin tolerant wheats. We identified Chuan Mai 25 (tolerant) and Ritchie (susceptible) as contrasting genotypes to metribuzin stress through dose-response analyses. Transcriptome sequencing using NovaSeq 6000 RNA-Seq platform identified a total of 77,443 genes; 59,915 known genes and 17,528 novel genes. The functional enrichment analysis at 0 h, 24 h and 60 h herbicide exposure revealed that endogenous increase of metabolic enzymes, light-harvesting chlorophyll proteins, PSII stability factor HCF136 and glucose metabolism conferred metribuzin tolerance. The validation of DEGs using RT-qPCR and QTL mapping confirmed their responsiveness to metribuzin. Transcription factors MYB, AP2-EREBP, ABI3VP1, bHLH, NAC are significantly expressed during metribuzin stress. Transcripts with significant enrichments revealed 114 SSRs for genomic selection. The master regulators provide promising avenues for enhancing metribuzin tolerance.

QTL Mapping Using a High-Density Genetic Map to Identify Candidate Genes Associated With Metribuzin Tolerance in Hexaploid Wheat (Triticum aestivum L.)

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.

Inheritance of pre-emergent metribuzin tolerance and putative gene discovery through high-throughput SNP array in wheat (Triticum aestivum L.)

BACKGROUND

Herbicide tolerance is an important trait that allows effective weed management in wheat crops in dryland farming. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we investigated gene effects for metribuzin tolerance in nine crosses of wheat by partitioning the means and variances of six basic generations from each cross into their genetic components to assess the gene action governing the inheritance of this trait. Metribuzin tolerance was measured by a visual senescence score 21 days after treatment. The wheat 90 K iSelect SNP genotyping assay was used to identify the distribution of alleles at SNP sites in tolerant and susceptible groups.

RESULTS

The scaling and joint-scaling tests indicated that the inheritance of metribuzin tolerance in wheat was adequately described by the additive-dominance model, with additive gene action the most significant factor for tolerance. The potence ratio for all the crosses ranged between - 1 and + 1 for senescence under metribuzin-treated conditions indicating a semi-dominant gene action in the inheritance of metribuzin tolerance in wheat. The number of segregating genes governing metribuzin tolerance was estimated between 3 and 15. The consistent high heritability range (0.82 to 0.92) in F_5-7 generations of Chuan Mai 25 (tolerant) × Ritchie (susceptible) cross indicated a significant contribution of additive genetic effects to metribuzin tolerance in wheat. Several genes related to photosynthesis (e.g. photosynthesis system II assembly factor YCF48), metabolic detoxification of xenobiotics and cell growth and development (cytochrome P450, glutathione S-transferase, glycosyltransferase, ATP-binding cassette transporters and glutathione peroxidase) were identified on different chromosomes (2A, 2D, 3B, 4A, 4B, 7A, 7B, 7D) governing metribuzin tolerance.

CONCLUSIONS

The simple additive-dominance gene effects for metribuzin tolerance will help breeders to select tolerant lines in early generations and the identified genes may guide the development of functional markers for metribuzin tolerance.